Gene expression profiling to identify druggable targets in prion diseases

Expert Opinion on Drug Discovery

Volumn 5, Issue 2, 2010, Pages 177-202

  Benetti, Federico ^a,b   Gasperini, Lisa ^a   Zampieri, Mattia ^a   Legname, Giuseppe ^a,b,c  

^a SISSA   (Italy)

^b ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

^c SINCROTRONE TRIESTE   (Italy)

Author keywords

Drug; Gene expression; Microarray; Prion

Indexed keywords

ABC TRANSPORTER A1; ACICLOVIR; ALOXISTATIN; ALPHA [AMINO(4 AMINOPHENYLTHIO)METHYLENE] 2 (TRIFLUOROMETHYL)PHENYLACETONITRILE; AMANTADINE; AMPHOTERICIN B; BETA 2 MICROGLOBULIN; BETA N ACETYLHEXOSAMINIDASE B; CATHEPSIN H; CATHEPSIN S; CHLOROQUINE; CLIOQUINOL; COMPLEMENT COMPONENT C1Q; DOXYCYCLINE; FC RECEPTOR; FILIPIN; FLUPIRTINE; GLIAL FIBRILLARY ACIDIC PROTEIN; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR; IMATINIB; LYMPHOCYTE ANTIGEN; MEPACRINE; MEPARTRICIN; METHOTREXATE; N [N (3 CARBOXYOXIRANE 2 CARBONYL)LEUCYL]AGMATINE; PENICILLAMINE; PENTOSAN POLYSULFATE; SURAMIN; TETRACYCLINE; UNINDEXED DRUG;

BOVINE SPONGIFORM ENCEPHALOPATHY; CLINICAL TRIAL; CREUTZFELDT JAKOB DISEASE; DRUG EFFECT; DRUG MECHANISM; DRUG TARGETING; ENCEPHALITIS; GENE EXPRESSION PROFILING; HUMAN; MICROARRAY ANALYSIS; NERVE DEGENERATION; NONHUMAN; PHARMACOGENOMICS; PRION DISEASE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEOMICS; REVIEW; TRANSCRIPTOMICS;

EID: 75449098078     PISSN: 17460441     EISSN: None     Source Type: Journal    
DOI: 10.1517/17460440903544449     Document Type: Review

References (97)

1. Prusiner SB. Prions. Proc Natl Acad Sci USA 1998;95(23):13363-13383
2. Doherr MG. Brief review on the epidemiology of transmissible spongiform encephalopathies (TSE). Vaccine 2007;25(30):5619-5624
3. Legname G, Baskakov IV, Nguyen HO, et al. Synthetic mammalian prions. Science 2004;305(5684):673-676
4. Hill AF, Antoniou M, Collinge J. Protease-resistant prion protein produced in vitro lacks detectable infectivity. J Gen Virol 1999;80(Pt 1):11-14
5. Cohen FE, Prusiner SB. Pathologic conformations of prion proteins. Annu Rev Biochem 1998;67:793-819
6. Telling GC, Parchi P, DeArmond SJ, et al. Evidence for the conformation of the pathologic isoform of the prion protein enciphering and propagating prion diversity. Science 1996;274(5295):2079-2082
7. Laurent M. Autocatalytic processes in cooperative mechanisms of prion diseases. FEBS Lett 1997;407(1):1-6
8. Telling GC, Haga T, Torchia M, et al. Interactions between wild-type and mutant prion proteins modulate neurodegeneration in transgenic mice. Genes Dev 1996;10(14):1736-1750
9. Kanaani J, Prusiner SB, Diacovo J, et al. Recombinant prion protein induces rapid polarization and development of synapses in embryonic rat hippocampal neurons in vitro. J Neurochem 2005;95(5):1373-1386
10. Lopes MH, Hajj GN, Muras AG, et al. Interaction of cellular prion and stress-inducible protein 1 promotes neuritogenesis and neuroprotection by distinct signaling pathways. J Neurosci 2005;25(49):11330-11339
11. Santuccione A, Sytnyk V, Leshchyns'ka I, Schachner M. Prion protein recruits its neuronal receptor NCAM to lipid rafts to activate p59fyn and to enhance neurite outgrowth. J Cell Biol 2005;169(2):341-354
12. Steele AD, Emsley JG, Ozdinler PH, et al. Prion protein (PrPc) positively regulates neural precursor proliferation during developmental and adult mammalian neurogenesis. Proc Natl Acad Sci USA 2006;103(9):3416-3421
13. Chen S, Mange A, Dong L, et al. Prion protein as trans-interacting partner for neurons is involved in neurite outgrowth and neuronal survival. Mol Cell Neurosci 2003;22(2):227-233
14. Bounhar Y, Zhang Y, Goodyer CG, LeBlanc A. Prion protein protects human neurons against Bax-mediated apoptosis. J Biol Chem 2001;276(42):39145-39149
15. Roucou X, Giannopoulos PN, Zhang Y, et al. Cellular prion protein inhibits proapoptotic Bax conformational change in human neurons and in breast carcinoma MCF-7 cells. Cell Death Differ 2005;12(7):783-795
16. Shyu WC, Chen CP, Saeki K, et al. Hypoglycemia enhances the expression of prion protein and heat-shock protein 70 in a mouse neuroblastoma cell line. J Neurosci Res 2005;80(6):887-894
17. Mitteregger G, Vosko M, Krebs B, et al. The role of the octarepeat region in neuroprotective function of the cellular prion protein. Brain Pathol 2007;17(2):174-183
18. Milhavet O, Lehmann S. Oxidative stress and the prion protein in transmissible spongiform encephalopathies. Brain Res Brain Res Rev 2002;38(3):328-339
19. Schmitt-Ulms G, Legname G, Baldwin MA, et al. Binding of neural cell adhesion molecules (N-CAMs) to the cellular prion protein. J Mol Biol 2001;314(5):1209-1225
20. Sales N, Rodolfo K, Hassig R, et al. Cellular prion protein localization in rodent and primate brain. Eur J Neurosci 1998;10(7):2464-2471
21. Sanchez-Alavez M, Conti B, Moroncini G, Criado JR. Contributions of neuronal prion protein on sleep recovery and stress response following sleep deprivation. Brain Res 2007;1158:71-80
22. Sanchez-Alavez M, Criado JR, Klein I, et al. Hypothalamic-pituitary- adrenal axis disregulation in PrPC-null mice. Neuroreport 2008;19(15):1473-1477
23. Tobler I, Gaus SE, Deboer T, et al. Altered circadian activity rhythms and sleep in mice devoid of prion protein. Nature 1996;380(6575):639-642
24. Rachidi W, Chimienti F, Aouffen M, et al. Prion protein protects against zinc-mediated cytotoxicity by modifying intracellular exchangeable zinc and inducing metallothionein expression. J Trace Elem Med Biol 2009;23(3):214-223
25. Nishida N, Tremblay P, Sugimoto T, et al. A mouse prion protein transgene rescues mice deficient for the prion protein gene from purkinje cell degeneration and demyelination. Lab Invest 1999;79(6):689-697
26. Caughey B, Brown K, Raymond GJ, et al. Binding of the protease-sensitive form of PrP (prion protein) to sulfated glycosaminoglycan and congo red [corrected]. J Virol 1994;68(4):2135-2141
27. Yang Y, Adelstein SJ, Kassis AI. Target discovery from data mining approaches. Drug Discov Today 2009;14(3-4):147-154
28. di Bernardo D, Thompson MJ, Gardner TS, et al. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol 2005;23(3):377-383
29. Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003;301(5629):102-105
30. Duguid JR, Rohwer RG, Seed B. Isolation of cDNAs of scrapie-modulated RNAs by subtractive hybridization of a cDNA library. Proc Natl Acad Sci USA 1988;85(15):5738-5742
31. Duguid JR, Bohmont CW, Liu NG, Tourtellotte WW. Changes in brain gene expression shared by scrapie and Alzheimer disease. Proc Natl Acad Sci USA 1989;86(18):7260-7264
32. Duguid JR, Dinauer MC. Library subtraction of in vitro cDNA libraries to identify differentially expressed genes in scrapie infection. Nucleic Acids Res 1990;18(9):2789-2792
33. Brenner M, Johnson AB, Boespflug-Tanguy O, et al. Mutations in GFAP, encoding glial fibrillary acidic protein, are associated with Alexander disease. Nat Genet 2001;27(1):117-120 (Pubitemid 32044531)
34. Rodriguez D, Gauthier F, Bertini E, et al. Infantile Alexander disease: spectrum of GFAP mutations and genotype-phenotype correlation. Am J Hum Genet 2001;69(5):1134-1140 (Pubitemid 33015827)
35. Aoki Y, Haginoya K, Munakata M, et al. A novel mutation in glial fibrillary acidic protein gene in a patient with Alexander disease. Neurosci Lett 2001;312(2):71-74
36. Sawaishi Y, Yano T, Takaku I, Takada G. Juvenile Alexander disease with a novel mutation in glial fibrillary acidic protein gene. Neurology 2002;58(10):1541-1543
37. Stumpf E, Masson H, Duquette A, et al. Adult Alexander disease with autosomal dominant transmission: a distinct entity caused by mutation in the glial fibrillary acid protein gene. Arch Neurol 2003;60(9):1307-1312
38. Brockmann K, Meins M, Taubert A, et al. A novel GFAP mutation and disseminated white matter lesions: adult Alexander disease? Eur Neurol 2003;50(2):100-105
39. Duguid J, Trzepacz C. Major histocompatibility complex genes have an increased brain expression after scrapie infection. Proc Natl Acad Sci USA 1993;90(1):114-117
40. Ebadi M, Iversen PL, Hao R, et al. Expression and regulation of brain metallothionein. Neurochem Int 1995;27(1):1-22
41. Karin M. Metallothioneins: proteins in search of function. Cell 1985;41(1):9-10
42. May PC, Finch CE. Sulfated glycoprotein 2: new relationships of this multifunctional protein to neurodegeneration. Trends Neurosci 1992;15(10):391-396
43. Stamatos C, Squicciarini J, Fine RE. Chick embryo spinal cord neurons synthesize a transferrin-like myotrophic protein. FEBS Lett 1983;153(2):387-390
44. Chowers I, Wong R, Dentchev T, et al. The iron carrier transferrin is upregulated in retinas from patients with age-related macular degeneration. Invest Ophthalmol Vis Sci 2006;47(5):2135-2140
45. Diedrich JF, Minnigan H, Carp RI, et al. Neuropathological changes in scrapie and Alzheimer's disease are associated with increased expression of apolipoprotein E and cathepsin D in astrocytes. J Virol 1991;65(9):4759-4768
46. Doh-ura K, Perryman S, Race R, Chesebro B. Identification of differentially expressed genes in scrapie-infected mouse neuroblastoma cells. Microb Pathog 1995;18(1):1-9
47. Cosseddu GM, Andreoletti O, Maestrale C, et al. Gene expression profiling on sheep brain reveals differential transcripts in scrapie-affected/not- affected animals. Brain Res 2007;1142:217-222
48. Baker CA, Manuelidis L. Unique inflammatory RNA profiles of microglia in Creutzfeldt-Jakob disease. Proc Natl Acad Sci USA 2003;100(2):675-679
49. Greenwood AD, Horsch M, Stengel A, et al. Cell line dependent RNA expression profiles of prion-infected mouse neuronal cells. J Mol Biol 2005;349(3):487-500
50. Martinez T, Pascual A. Identification of genes differentially expressed in SH-SY5Y neuroblastoma cells exposed to the prion peptide 106-126. Eur J Neurosci 2007;26(1):51-59
51. Xiang W, Windl O, Westner IM, et al. Cerebral gene expression profiles in sporadic Creutzfeldt-Jakob disease. Ann Neurol 2005;58(2):242-257
52. Julius C, Hutter G, Wagner U, et al. Transcriptional stability of cultured cells upon prion infection. J Mol Biol 2008;375(5):1222-1233
53. Bach C, Gilch S, Rost R, et al. Prion-induced activation of cholesterogenic gene expression by Srebp2 in neuronal cells. J Biol Chem 2009;284(45):31260-31269
54. Brown AR, Webb J, Rebus S, et al. Identification of up-regulated genes by array analysis in scrapie-infected mouse brains. Neuropathol Appl Neurobiol 2004;30(5):555-567
55. Brown AR, Rebus S, McKimmie CS, et al. Gene expression profiling of the preclinical scrapie-infected hippocampus. Biochem Biophys Res Commun 2005;334(1):86-95
56. Riemer C, Neidhold S, Burwinkel M, et al. Gene expression profiling of scrapie-infected brain tissue. Biochem Biophys Res Commun 2004;323(2):556-564
57. Xiang W, Hummel M, Mitteregger G, et al. Transcriptome analysis reveals altered cholesterol metabolism during the neurodegeneration in mouse scrapie model. J Neurochem 2007;102(3):834-847
58. Booth S, Bowman C, Baumgartner R, et al. Identification of central nervous system genes involved in the host response to the scrapie agent during preclinical and clinical infection. J Gen Virol 2004;85(Pt 11):3459-3471
59. Sorensen G, Medina S, Parchaliuk D, et al. Comprehensive transcriptional profiling of prion infection in mouse models reveals networks of responsive genes. BMC Genomics 2008;9:114
60. Skinner PJ, Abbassi H, Chesebro B, et al. Gene expression alterations in brains of mice infected with three strains of scrapie. BMC Genomics 2006;7:114
61. Xiang W, Windl O, Wunsch G, et al. Identification of differentially expressed genes in scrapie-infected mouse brains by using global gene expression technology. J Virol 2004;78(20):11051-11060
62. Miele G, Seeger H, Marino D, et al. Urinary alpha1-antichymotrypsin: a biomarker of prion infection. PLoS One 2008;3(12):e3870
63. Hwang D, Lee IY, Yoo H, et al. A systems approach to prion disease. Mol Syst Biol 2009;5:252
64. Gehlenborg N, Hwang D, Lee IY, et al. The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases. Database 2009, doi: 10.1093/database/bap011
65. Moody LR, Herbst AJ, Yoo HS, et al. Comparative prion disease gene expression profiling using the prion disease mimetic, cuprizone. Prion 2009;3(2):99-109
66. Russelakis-Carneiro M, Saborio GP, Anderes L, Soto C. Changes in the glycosylation pattern of prion protein in murine scrapie. Implications for the mechanism of neurodegeneration in prion diseases. J Biol Chem 2002;277(39):36872-36877
67. Barret A, Forestier L, Deslys JP, et al. Glycosylation-related gene expression in prion diseases: PrPSc accumulation in scrapie infected GT1 cells depends on beta-1,4-linked GalNAc-4-SO4 hyposulfation. J Biol Chem 2005;280(11):10516-10523
68. Guillerme-Bosselut F, Forestier L, Jayat-Vignoles C, et al. Glycosylation-related gene expression profiling in the brain and spleen of scrapie-affected mouse. Glycobiology 2009;19(8):879-889
69. Aguzzi A, Heikenwalder M. Pathogenesis of prion diseases: current status and future outlook. Nat Rev Microbiol 2006;4:765-775
70. Comelli EM, Head SR, Gilmartin T, et al. A focused microarray approach to functional glycomics: transcriptional regulation of the glycome. Glycobiology 2006;16(2):117-131
71. Costa C, Tortosa R, Vidal E, et al. Central nervous system extracellular matrix changes in a transgenic mouse model of bovine spongiform encephalopathy. Vet J 2009;182(2):306-314
72. Ritchie MA, Gill AC, Deery MJ, Lilley K. Precursor ion scanning for detection and structural characterization of heterogeneous glycopeptide mixtures. J Am Soc Mass Spectrom 2002;13(9):1065-1077
73. Sawiris GP, Becker KG, Elliott EJ, et al. Molecular analysis of bovine spongiform encephalopathy infection by cDNA arrays. J Gen Virol 2007;88(Pt 4):1356-1362
74. Tang Y, Xiang W, Hawkins SA, et al. Transcriptional changes in the brains of cattle orally infected with the bovine spongiform encephalopathy agent precede detection of infectivity. J Virol 2009;83(18):9464-9473
75. Sakaguchi S. Recent developments in therapeutics for prion disease. Expert Opin Ther Patents 2008;18(1):35-39
76. Brajtburg J, Elberg S, Bolard J, et al. Interaction of plasma proteins and lipoproteins with amphotericin B. J Infect Dis 1984;149(6):986-997
77. Pocchiari M, Casaccia P, Ladogana A. Amphotericin B: a novel class of antiscrapie drugs. J Infect Dis 1989;160(5):795-802
78. Trevitt CR, Collinge J. A systematic review of prion therapeutics in experimental models. Brain 2006;129(Pt 9):2241-2265
79. Masullo C, Macchi G, Xi YG, Pocchiari M. Failure to ameliorate Creutzfeldt-Jakob disease with amphotericin B therapy. J Infect Dis 1992;165(4):784-785
80. Stewart LA, Rydzewska LH, Keogh GF, Knight RS. Systematic review of therapeutic interventions in human prion disease. Neurology 2008;70(15):1272- 1281
81. Sviridov D, Nestel P, Watts G. Statins and metabolism of high density lipoprotein. Cardiovasc Hematol Agents Med Chem 2007;5(3):215-221
82. Taraboulos A, Scott M, Semenov A, et al. Cholesterol depletion and modification of COOH-terminal targeting sequence of the prion protein inhibit formation of the scrapie isoform. J Cell Biol 1995;129(1):121-132
83. Bate C, Salmona M, Diomede L, Williams A. Squalestatin cures prion-infected neurons and protects against prion neurotoxicity. J Biol Chem 2004;279(15):14983-14990
84. Mok SW, Thelen KM, Riemer C, et al. Simvastatin prolongs survival times in prion infections of the central nervous system. Biochem Biophys Res Commun 2006;348(2):697-702
85. Kempster S, Bate C, Williams A. Simvastatin treatment prolongs the survival of scrapie-infected mice. Neuroreport 2007;18(5):479-482
86. Doh-Ura K, Iwaki T, Caughey B. Lysosomotropic agents and cysteine protease inhibitors inhibit scrapie-associated prion protein accumulation. J Virol 2000;74(10):4894-4897
87. Caughey B, Raymond GJ. Sulfated polyanion inhibition of scrapie-associated PrP accumulation in cultured cells. J Virol 1993;67(2):643-650
88. Engelstein R, Grigoriadis N, Greig NH, et al. Inhibition of P53-related apoptosis had no effect on PrP(Sc) accumulation and prion disease incubation time. Neurobiol Dis 2005;18(2):282-285
89. Perovic S, Schroder HC, Pergande G, et al. Effect of flupirtine on Bcl-2 and glutathione level in neuronal cells treated in vitro with the prion protein fragment (PrP106-126). Exp Neurol 1997;147(2):518-524
90. Otto M, Cepek L, Ratzka P, et al. Efficacy of flupirtine on cognitive function in patients with CJD: a double-blind study. Neurology 2004;62(5):714-718
91. Kocisko DA, Baron GS, Rubenstein R, et al. New inhibitors of scrapie-associated prion protein formation in a library of 2000 drugs and natural products. J Virol 2003;77(19):10288-10294
92. Drisko JA. The use of antioxidants in transmissible spongiform encephalopathies: a case report. J Am Coll Nutr 2002;21(1):22-25
93. Soiland H, Soreide K, Janssen EA, et al. Emerging concepts of apolipoprotein D with possible implications for breast cancer. Cell Oncol 2007;29(3):195-209
94. Nordstrom E, Fisone G, Kristensson K. Opposing effects of ERK and p38-JNK MAP kinase pathways on formation of prions in GT1-1 cells. FASEB J 2009;23(2):613-622
95. Sigurdsson EM, Brown DR, Alim MA, et al. Copper chelation delays the onset of prion disease. J Biol Chem 2003;278(47):46199-46202
96. Hijazi N, Shaked Y, Rosenmann H, et al. Copper binding to PrPC may inhibit prion disease propagation. Brain Res 2003;993(1-2):192-200
97. Orem NR, Geoghegan JC, Deleault NR, et al. Copper (II) ions potently inhibit purified PrPres amplification. J Neurochem 2006;96(5):1409-1415