Gene expression analysis of frontotemporal lobar degeneration of the motor neuron disease type with ubiquitinated inclusions

Acta Neuropathologica

Volumn 114, Issue 1, 2007, Pages 81-94

  Mishra, Manjari ^a   Paunesku, Tatjana ^a   Woloschak, Gayle E ^a   Siddique, Teepu ^a   Zhu, Lihua ^a   Lin, Simon ^a   Greco, Kristin ^a   Bigio, Eileen H ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Amyotrophic lateral sclerosis; Dementia; Frontotemporal lobar degeneration; Gene expression; Microarray; Motor neuron disease; qRT PCR; Ubiquitin

Indexed keywords

DYNEIN ADENOSINE TRIPHOSPHATASE; LIPOCORTIN 2; MYELOID DIFFERENTIATION FACTOR 88; PROGRANULIN; PROTEASOME; UBIQUITIN;

ADULT; AGED; APOPTOSIS; ARTICLE; AUTOPSY; CELL INCLUSION; CELL SELECTION; CLINICAL ARTICLE; CONTROLLED STUDY; CYTOSKELETON; DEGENERATIVE DISEASE; ENDOSOME; FEMALE; FRONTAL CORTEX; FRONTOTEMPORAL LOBAR DEGENERATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC CODE; GENETIC LINKAGE; GENETIC SCREENING; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; MALE; MICROARRAY ANALYSIS; MICROTUBULE; MOTONEURON; MOTOR NEURON DISEASE; PRIORITY JOURNAL; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SIGNAL TRANSDUCTION; SYNAPSE; UBIQUITINATION; VALIDATION STUDY;

AGED; ANNEXIN A2; CASE-CONTROL STUDIES; DEMENTIA; DNA-BINDING PROTEINS; DYNEIN ATPASE; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; INCLUSION BODIES; INTERCELLULAR SIGNALING PEPTIDES AND PROTEINS; MALE; MIDDLE AGED; MOTOR NEURON DISEASE; MYELOID DIFFERENTIATION FACTOR 88; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; UBIQUITIN;

EID: 34447099071     PISSN: 00016322     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00401-007-0240-7     Document Type: Article

References (65)

1. Alter O, Brown PO, Botstein D (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 97:10101-10106
2. Arai T, Hasegawa M, Akiyama H, Ikeda K, Nonaka T, Mori H, Mann D, Tsuchiya K, Yoshida M, Hashizume Y, Oda T (2006) TDP-43 is a component of ubiquitin-positive tau-negative inclusions in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Biochem Biophys Res Commun 351:602-611
3. Ayala YM, Pantano S, Ambrogio AD, Buratti E, Brindisi A, Marchetti C, Romano M, Baralle FE (2005) Human, Drosophila, and C. elegans TDP43: nucleic acid binding properties and splicing regulatory function. J Mol Biol 348:575-588
4. Baker M, Mackenzie IRA, Pickering-Brown S, Gass J, Rademakers R, Lindholm C, Snowden J, Adamson J, Sadovnick AD, Rollison S, Cannon A, Dwosh E, Neary D, Melquist S, Richardson A, Dickson D, Berger Z, Eriksen J, Robinson T, Zehr C, Dickey CA, Crook R, McGowan E, Mann D, Boeve B, Feldman H, Hutton M (2006) Mutations in progranulin cause tau-negative frontotemporal dementia linked to chromosome 17. Nature 442:916-919
5. Behrens MI, Mukherjee O, Tu PH, Liscic RM, Grinberg LT, Carter D, Paulsmeyer K, Taylor-Reinwald L, Gritcho M, Norton JB, Chakraverty S, Goate AM, Morris JC, Cairns NJ (2007) Neuropathologic heterogeneity in HDDD1: A familial frontotemporal lobar degeneration with ubiquitin-positive inclusions and progranulin mutation. Alz Dis Assoc Disord (in press)
6. Benussi L, Binetti G, Sina E, Gigola L, Bettecken T, Meitinger T, Ghidoni R (2006) A novel deletion in progranulin gene is associated with FTDP-17 and CBS. Neurobiol Aging. doi 10.1016/ j.neurobiolaging.2006.10.028
7. Bigio EH, Johnson NA, Rademaker AW, Fung BB, Mesulam MM, Siddique N, Dellafave L, Caliendo J, Freeman S, Siddique T (2004) Neuronal ubiquitinated intranuclear inclusions in familial and non-familial frontotemporal dementia of the motor neuron disease type associated with amyotrophic lateral sclerosis. J Neuropathol Exp Neurol 63:801-811
8. Boeve BF, Baker M, Dickson DW, Parisi JE, Giannini C, Joesephs KA, Hutton M, Pickering-Brown SM, Rademakers R, Tang-Wai D, Jack CR Jr, Kantarci K, Shiung MM, Golde T, Smith GE, Greda YE, Knopman DS, Petersen RC (2006) Frontotemporal dementia and parkinsonism associated with the IVSI + IG → a mutation in progranulin: A clinicopathologic study. Brain 129:3103-3114
9. Buesa C, Maes T, Subirada F, Barrachina M, Ferrer I (2004) DNA Chip technology in brain banks: Confronting a degrading world. J Neuropathol Exp Neurol 63:1003-1014
10. Butte A (2002) The use and analysis of microarray data. Nat Rev Drug Discov 1:951-960
11. Cairns NJ, Zhukareva V, Uryu K, Zhang B, Bigio E, Mackenzie IR, Gearing M, Duyckaerts C, Yokoo H, Nakazato Y, Jaros E, Perry RH, Lee VM, Trojanowski JQ (2004) Alpha-internexin is present in the pathological inclusions of neuronal intermediate filament inclusion disease. Am J Pathol 164:2153-2161
12. Caspersen C, Wang N, Yao J, Sosunov A, Chen X, Lustbader JW, Xu HW, Stern D, McKhann G, Yan SD (2005) Mitochondrial A {beta}: A potential focal point for neuronal metabolic dysfunction in Alzheimer's disease. FASEB J 19:2040-2041
13. Celentano JJ, Gyenes M, Gibbs TT, Farb DH (1991) Negative modulation of the γ-aminobutyric acid response by extracellular zinc. Mol Pharmacol 40:766-773
14. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156-159
15. Cooper PN, Jackson M, Lennox G, Lowe J, Mann DM (1995) Tau, ubiquitin, and alpha B-crystallin immunohistochemistry define the principal causes of degenerative frontotemporal dementia. Arch Neurol 52:1011-1015
16. Cruts M, Gijselink I, Van Der Zee J, Engelbirghs S, Wils H, Pirici D, Rademakers R, Vandenberghe R, Dermaut B, Jean-Jacques M, Van Duijn C, Peeters K, Sciot R, Santens P, Pooter TD, Mattheijssens M, Van den Broeck M, Cuijt I, Vennekens K, De Deyn PP, Singh SK, Ven Broeckhoven CV (2006) Null mutations in progranulin cause ubiquitin-positive frontotemporal dementia linked to chromosome 17q21. Nature 442:920-924
17. Davidson Y, Kelley T, Mackenzie IRA, Pickering-Brown S, Plessis DD, Neary D, Snowden JS, Mann DA (2007) Ubiquitinated pathological lesions in frontotemporal lobar degeneration contain the TAR DNA-binding protein, TDP-43. Acta Neuropathol 113:521-533
18. Davion S, Johnson N, Weintraub S, Mesulam M-M, Engberg A, Mishra M, Baker M, Adamson J, Hutton M, Rademakers R, Bigio EH (2007) Clinicopathologic correlation in PGRN mutations. Neurology (in press)
19. De Vrij FM, Sluijs JA, Gregori L, Fischer DF, Hermens WT, Goldgaber D, Verhaagen J, Van Leeuwan FW, Hol EM (2001) Mutant ubiquitin expressed in Alzheimer's disease causes neuronal death. FASEB J 15:2680-2688
20. Dickey CA, Loring JF, Montgomery J, Gordon MN, Eastman PS, Morgan D (2003) Selectively reduced expression of synaptic plasticity-related genes in amyloid precursor protein + presenilin-1 transgenic mice. J Neurosci 23:5219-5226
21. DNA chip analyzer software. Updated Oct. 2005 available at http://www.dchip.org. Accessed December 2005
22. Ebadi M, Iversen PL, Hao R, Cerutis DR, Rojas P, Happe HK, Murrin LC, Pfeiffer RF (1995) Expression and regulation of brain metallothionein. Neurochem Int 27:1-22
23. Editorial. Dementia and motoneurone disease (1990) Lancet 335:1250-1252
24. Eisen MB, Spellman PT, Brown PO, Boltstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863-14868
25. Evans SJ, Choudary PV, Vawter MP, Li J, Meador-Woodruff JH, Lopez JF, Burke SM, Thompson RC, Myers RM, Jones EG, Bunney WE, Watson SJ, Akil H (2004) DNA microarray analysis of functionally discrete human brain regions reveals divergent transcriptional profiles. Neurobiol Dis 14:240-250
26. Fischer DF, De Vos RA, Van Dijk R, De Vrij FM, Proper EA, Sonnemans MA, Verhage MC, Sluijs JA, Hobo B, Zouambia M, Steur EN, Kamphorst W, Hol EM, Van Leeuwan FW (2003) Disease-specific accumulation of mutant ubiquitin as a marker for proteasomal dysfunction in the brain. FASEB J 17:2014-2024
27. Forman MS, Trojanowski JQ, Lee VM (2004) Neurodegenerative diseases: A decade of discoveries paves the way for therapeutic breakthroughs. Nat Med 10:1055-1063
28. GEO datasets available at NIH website http://www.ncbi.nlm.nih.gov. Accessed Feb 2006
29. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CO, Lander ES (1999) Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286:531-537
30. Hudson AJ (1981) Amyotrophic lateral sclerosis and its association with dementia, parkinsonism and other neurological disorders: A review. Brain 104:217-247
31. IntAct protein interaction Database available at website http://www.ebi.ac.uk/intact/search/do/search?searchstring=Q13148. Acessed Feb 2007
32. Iseki E, Li F, Odawara T, Hino H, Suzuki K, Kosaka K, Akiyama H, Ikeda K, Kato M (1998) Ubiquitin-immunohistochemical investigation of atypical Pick's disease without Pick bodies. J Neurol Sci 159:194-201
33. Jackson M, Lowe J (1996) The new neuropathology of degenerative frontotemporal dementias. Acta Neuropathol 91:127-134
34. Kertesz A, Kawarai T, Rogaeva E, St George-Hyslop P, Bird TD, Munoz DG (2000) Familial frontotemporal dementia with ubiquitin-positive, tau-negative inclusions. Neurology 54:818-827
35. Lam YA, Pickart CM, Alban A, Landon M, Jamieson C, Ramage R, Mayer RJ, Layfield R (2000) Inhibition of the ubiquitin-proteasome system in Alzheimer's disease. Proc Natl Acad Sci USA 97:9902-9906
36. Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31-36
37. Lindsten K, de Vrij FM, Verhoef LG, Fiscer DF, Van Leuuwan FW, Hol EM, Masucci MG, Dantuma NP (2002) Mutant ubiquitin found in neurodegenerative disorders is a ubiquitin fusion degradation substrate that blocks proteosomal degradation. J Cell Biol 157:417-427
38. Lockhart DJ, Barlow C (2001) Expressing what's on your mind: DNA arrays and the brain. Nat Rev 2:63-68
39. Mackenzie IRA, Baborie A, Pickering-Brown SM, Plessis DD, Jaros E, Perry RH, Neary D, Snowden JS, Mann DMA (2006) Heterogeneity of ubiquitin pathology in frontotemporal lobar degeneration: Classification and relation to clinical phenotype. Acta Neuropathol 112:539-549
40. Mackenzie IRA, Baker M, Pickering-Brown SM, Ging-Yuek R, Lindholm C, Dwosh E, Gass J, Cannon A, Rademakers R, Hutton M, Feldman HH (2006) The neuropathology of frontotemporal lobar degeneration caused by mutations in the progranulin gene. Brain 129:3081-3090
41. Masellis M, Momeni P, Meschino W, Heffner R Jr, Elder J, Sato C, Liang Y, St George-Hyslop P, Hardy J, Bilbao J, Black S, Rogaeva E (2006) Novel splicing mutation in the progranulin gene causing familial corticobasal syndrome. Brain 129:2808-2810
42. Mayer RJ (2003) From neurodegeneration to neurohomeostasis: The roles of ubiquitin. Drug News Perspect 16:103-108
43. McKhann GM, Albert MS, Grossman M, Miller B, Dickson D, Trojanowski JQ (2001) Clinical and pathological diagnosis of frontotemporal dementia: report of the work group on frontotemporal dementia and Pick's disease. Arch Neurol 58:1803-1809
44. Mesulam M, Johnson N, Krefft TA, Gass JM, Ashley D, Cannon BS, Adamson J, Bigio EH, Weintraub S, Dickson DW, Hutton ML, Graff-Radford NR (2007) Progranulin mutations in primary progressive aphasia - the PPA1 and PPA3 families. Arch Neurol 64:43-47
45. Morita K, Kaiya H, Ikeda T, Namba M (1987) Presenile dementia combined with amyotrophy: A review of 34 Japanese cases. Arch Gerontol Geriatr 6:263-277
46. Mukherjee O, Pastor P, Cairns N, Chakraverty S, Kauwe JS, Shears S, Behrens MI, Budde J, Hinrichs AL, Norton J, Levitch D, Taylor-Reinwald L, Gitcho M, Tu PH, Tenenholz Grinberg L, Liscic RM, Armendariz J, Morris JC, Goate AM (2006) HDDD2 is a familial FTLD-U caused by a missense mutation in progranulin. Ann Neurol 60:314-322
47. Neumann M, Sampathu DM, Kwong LK, Chou TT, Traux AC, Micsenyi MC, Chou TT, Bruce J, Schuck T, Grossman M, Clark CM, McCluskey LF, Miller BM, Masliah E, Mackenzie IR, Feldman H, Feiden W, Kretzschmar HA, Trojanowski JQ, Lee VM (2006) Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Science 314:130-133
48. Neumann M, Mackenzie IRA, Cairns NJ, Boyer PJ, Markesbery WR, Smith CD, Taylor JP, Kretzchmar HA, Kimonis VE, Forman MS (2007) TDP-43 in the ubiquitin pathology of frontotemporal dementia with VCP gene mutations. J Neuropathol Exp Neurol 66:152-157
49. Neumann M, Kwong LK, Truax AC, Vanmassenhove B, Kretzschmar HA, Van Deerlin VM, Clark CM, Grossman M, Miller BL, Trojanowski JQ, Lee VMY (2007) TDP-43-positive white matter pathology in frontotemporal lobar degeneration with ubiquitin-positive inclusions. J Neuropathol Exp Neurol 66:177-183
50. Okamoto K, Hirai S, Yamazaki T, Sun XY, Nakazato Y (1991) New ubiquitin-positive intraneuronal inclusion in the extra-motor cortices in patients with amyotrophic lateral sclerosis. Neurosci Lett 129:233-236
51. Pickering-Brown SM, Baker M, Gass J, Boeve BF, Loy CT, Brooks WS, Mackenzie IRA, Martins RN, Kwok JBJ, Halliday GM, Kril J, Schofield PR, Mann DMA, Hutton M (2006) Mutations in progranulin explain atypical phenotypes with variants in MAPT. Brain 129:3124-3126
52. Rademakers R, Cruts M, Dermaut B, Sleegers K, Rosso SM, Van den Broeck M, Backhovens H, Van Swieten J, Van Duijn CM, Van Broeckhoven C (2002) Tau negative frontal lobe dementia at 17q21: Significant finemapping of the candidate region to a 4.8 cm interval. Mol Psychiatry 7:1064-1074
53. Raychaudhuri S, Stuart JM, Altman RB (2000) Principal components analysis to summarize microarray experiments: Application to sporulation time series. Pac Symp Biocomput 455-66
54. Rideout HJ, Larsen KE, Sulzer D, Stefanis L (2001) Proteasomal inhibition leads to formation of ubiquitin/ alpha-synuclein-immunoreactive inclusions in PC12 cells. J Neurochem 78:899-908
55. Rowan MJ, Klyubin I, Wang Q, Anwyl R (2005) Synaptic plasticity disruption by amyloid beta protein: Modulation by potential Alzheimer's disease modifying therapies. Biochem Soc Trans 33:563-567
56. Sampathu DM, Neumann M, Kwong LK, Chou TT, Micsenyi M, Truax A, Bruce J, Grossman M, Trojanowski JQ, Lee VMY (2006) Pathological heterogeneity of frontotemporal lobar degeneration with ubiquitin-positive inclusions delineated by ubiquitin immunohistochemistry and novel monoclonal antibodies. Am J Pathol 169:1343-1352
57. Schroder R, Watts GD, Mehta SG, Evert BO, Broich P, Fleissbach K, Pauls K, Hans VH, Kimonis V, Thal DR (2005) Mutant valosin-containing protein causes a novel type of frontotemporal dementia. Ann Neurol 57:457-461
58. Snowden JS, Pichering-Brown SM, Mackenzie IRA, Richardson AMT, Verma A, Neary D, Mann DMA (2006) Progranulin gene mutations associated with frontotemporal dementia and progressive non-fluent aphasia. Brain 129:3091-3102
59. Terry RD, Masliah E, Salmon DP, Butters N, DeTeresa R, Hill R, Hansen LA, Katzman R (1991) Physical basis of cognitive alterations in Alzheimer's disease: Synapse loss is the major correlate of cognitive impairment. Ann Neurol 30:572-580
60. Trojanowski JQ, Dickson D (2001) Update on the neuropathological diagnosis of frontotemporal dementias. J Neuropathol Exp Neurol 60:1123-1126
61. Tsuchiya K, Ikeda K, Haga C, Kobayashi T, Morimatsu Y, Nakano I, Matsushita M (2001) Atypical amyotrophic lateral sclerosis with dementia mimicking frontal Pick's disease: A report of an autopsy case with a clinical course of 15 years. Acta Neuropathol 101:625-630
62. Vincent VAM, DeVoss JJ, Ryan HS, Murphy GM (2002) Analysis of neuronal gene expression with laser capture microdissection. J Neurosci Res 69:578-586
63. Wightman G, Anderson VE, Martin J, Swash M, Anderton BH, Neary D, Mann D, Luthert P, Leigh PN (1992) Hippocampal and neocortical ubiquitin-immunoreactive inclusions in amyotrophic lateral sclerosis with dementia. Neurosci Lett 139:269-274
64. Wikstrom J, Paetau A, Palo J, Sulkava R, Haltia M (1982) Classic amyotrophic lateral sclerosis with dementia. Arch Neurol 39:681-683
65. Wurmbach E, Gonzalez-Maeso J, Yuen T, Ebersole BJ, Mastaitis JW, Mobbs CV, Sealfon SC (2002) Validated genomic approach to study differentially expressed genes in complex tissues. Neurochem Res 27:1027-1033