Alzheimer's & Dementia: The Journal of the Alzheimer's Association
Volume 6, Issue 1 , Pages 25-38 , January 2010

Toward an Alzheimer's disease diagnosis via high-resolution blood gene expression

References 

  1. Patterson C, Feightner JW, Garcia A, Hsiung GY, MacKnight C, Sadovnick AD. Diagnosis and treatment of dementia: 1. Risk assessment and primary prevention of Alzheimer disease.
  2. Lee C, Wang Q. Bioinformatics analysis of alternative splicing. Brief Bioinform. 2005;6:23–33
  3. Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS, et al. Human Gene Mutation Database (HGMD): 2003 update. Hum Mutat. 2003;21:577–581
  4. Span PN, Tjan-Heijnen VC, Heuvel JJ, de Kok JB, Foekens JA, Sweep FC. Do the survivin (BIRC5) splice variants modulate or add to the prognostic value of total survivin in breast cancer?. Clin Chem. 2006;52:1693–1700
  5. Yeo G, Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome Biol. 2004;5:R74
  6. Li Q, Lee J-A, Black DL. Neuronal regulation of alternative pre-mRNA splicing. Nat Rev Neurosci. 2007;8:819–831
  7. Shirotani K, Tomioka M, Kremmer E, Haass C, Steiner H. Pathological activity of familial Alzheimer's disease-associated mutant presenilin can be executed by six different gamma-secretase complexes. Neurobiol Dis. 2007;27:102–107
  8. Heinzen EL, Yoon W, Weale ME, Sen A, Wood NW, Burke JR, et al. Alternative ion channel splicing in mesial temporal lobe epilepsy and Alzheimer's disease. Genome Biol. 2007;8:R32
  9. Glatz DC, Rujescu D, Tang Y, Berendt FJ, Hartmann AM, Faltraco F, et al. The alternative splicing of tau exon 10 and its regulatory proteins CLK2 and TRA2-BETA1 changes in sporadic Alzheimer's disease. J Neurochem. 2006;96:635–644
  10. Manabe T, Katayama T, Sato N, Gomi F, Hitomi J, Yanagita T, et al. Induced HMGA1a expression causes aberrant splicing of presenilin-2 pre-mRNA in sporadic Alzheimer's disease. Cell Death Differ. 2003;10:698–708
  11. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. JR Statis Soc [B]. 1995;57:289–300
  12. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, et al. The MicroArray Quality Control (MAQC) Project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006;24:1151–1161
  13. Shippy R, Fulmer-Smentek S, Jensen RV, Jones WD, Wolber PK, Johnson CD, et al. Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol. 2006;24:1123–1131
  14. Einstein R, Jordan H, Zhou W, Brenner M, Moses EG, Liggett SB. Alternative splicing of the G protein-coupled receptor superfamily in human airway smooth muscle diversifies the complement of receptors. Proc Natl Acad Sci USA. 2008;105:5230–5235
  15. Filippov V, Schmidt EL, Filippova M, Duerksen-Hughes PJ. Splicing and splice factor SRp55 participate in the response to DNA damage by changing isoform ratios of target genes. Gene. 2008;420:34–41
  16. Hewetson A, Wright-Pastusek AE, Helmer RA, Wesley KA, Chilton BS. Conservation of inter-protein sites in RUSH and RFBP, an ATP11B isoform. Mol Cell Endocrinol. 2008;292:79–86
  17. Andre F, Michiels S, Dessen P, Scott V, Suciu V, Lazar V, et al. Exonic expression profiling of breast cancer and benign lesions: a retrospective analysis. Lancet Oncol. 2009 Apr;10(4):381–390Epub 2009 Feb 25
  18. Noble WS. What is a support vector machine?. Nat Biotechnol. 2006;24:1565–1567
  19. Tan J, Town T, Abdullah L, Wu Y, Placzek A, Small B, et al. CD45 isoform alteration in CD4+ T cells as a potential diagnostic marker of Alzheimer's disease. J Neuroimmunol. 2002;132:164–172
  20. Kamino K, Nagasaka K, Imagawa M, Yamamoto H, Yoneda H, Ueki A, et al. Deficiency in mitochondrial aldehyde dehydrogenase increases the risk for late-onset Alzheimer's disease in the Japanese population. Biochem Biophys Res Commun. 2000;273:192–196
  21. Franchi L, Park JH, Shaw MH, Marina-Garcia N, Chen G, Kim YG, et al. Intracellular NOD-like receptors in innate immunity, infection and disease. Cell Microbiol. 2008;10:1–8
  22. Minoda Y, Saeki K, Aki D, Takaki H, Sanada T, Koga K, et al. A novel zinc finger protein, ZCCHC11, interacts with TIFA and modulates TLR signaling. Biochem Biophys Res Commun. 2006;344:1023–1030
  23. Akira S, Hoshino K, Kaisho T. The role of Toll-like receptors and MyD88 in innate immune responses. J Endotoxin Res. 2000;6:383–387
  24. Kim OS, Park EJ, Joe EH, Jou I. JAK-STAT signaling mediates gangliosides-induced inflammatory responses in brain microglial cells. J Biol Chem. 2002;277:40594–40601
  25. Kelliher M, Fastbom J, Cowburn RF, Bonkale W, Ohm TG, Ravid R, et al. Alterations in the ryanodine receptor calcium release channel correlate with Alzheimer's disease neurofibrillary and beta-amyloid pathologies. Neuroscience. 1999;92:499–513
  26. Vollbach H, Heun R, Morris CM, Edwardson JA, McKeith IG, Jessen F, et al. APOA1 polymorphism influences risk for early-onset nonfamiliar AD. Ann Neurol. 2005;58:436–441
  27. Duchateau PN, Pullinger CR, Orellana RE, Kunitake ST, Naya-Vigne J, O'Connor PM, et al. Apolipoprotein L, a new human high density lipoprotein apolipoprotein expressed by the pancreas. Identification, cloning, characterization, and plasma distribution of apolipoprotein L. J Biol Chem. 1997;272:25576–25582
  28. Lee MH, Lu K, Hazard S, Yu H, Shulenin S, Hidaka H, et al. Identification of a gene, ABCG5, important in the regulation of dietary cholesterol absorption. Nat Genet. 2001;27:79–83
  29. Wenzel JJ, Kaminski WE, Piehler A, Heimerl S, Langmann T, Schmitz G. ABCA10, a novel cholesterol-regulated ABCA6-like ABC transporter. Biochem Biophys Res Commun. 2003;306:1089–1098
  30. Ma SL, Ng HK, Baum L, Pang JC, Chiu HF, Woo J, et al. Low-density lipoprotein receptor-related protein 8 (apolipoprotein E receptor 2) gene polymorphisms in Alzheimer's disease. Neurosci Lett. 2002;332:216–218
  31. Scherzer CR, Eklund AC, Morse LJ, Liao Z, Locascio JJ, Fefer D, et al. Molecular markers of early Parkinson's disease based on gene expression in blood. Proc Natl Acad Sci USA. 2007;104:955–960
  32. Hoe HS, Wessner D, Beffert U, Becker AG, Matsuoka Y, Rebeck GW. F-spondin interaction with the apolipoprotein E receptor ApoEr2 affects processing of amyloid precursor protein. Mol Cell Biol. 2005;25:9259–9268
  33. Carter CJ. Convergence of genes implicated in Alzheimer's disease on the cerebral cholesterol shuttle: APP, cholesterol, lipoproteins, and atherosclerosis. Neurochem Int. 2007;50:12–38
  34. Gombos I, Kiss E, Detre C, László G, Matkó J. Cholesterol and sphingolipids as lipid organizers of the immune cells' plasma membrane: their impact on the functions of MHC molecules, effector T-lymphocytes and T-cell death. Immunol Lett. 2006;104:59–69
  35. Shimizu T, Matsuoka Y, Shirasawa T. Biological significance of isoaspartate and its repair system. Biol Pharm Bull. 2005;28:1590–1596
  36. Watanabe A, Takio K, Ihara Y. Deamidation and isoaspartate formation in smeared tau in paired helical filaments. Unusual properties of the microtubule-binding domain of tau. J Biol Chem. 1999;274:7368–7378
  37. Hull J, Campino S, Rowlands K, Chan MS, Copley RR, Taylor MS, et al. Identification of common genetic variation that modulates alternative splicing. PLoS Genet. 2007;3:e99
  38. Kwan T, Benovoy D, Dias C, Gurd S, Provencher C, Beaulieu P, et al. Genome-wide analysis of transcript isoform variation in humans. Nat Genet. 2008;40:225–231
  39. Ishunina TA, Swaab DF. Estrogen receptor-alpha splice variants in the human brain. Gynecol Endocrinol. 2008;24:93–98
  40. Simonyi A, Ngomba RT, Storto M, Catania MV, Miller LA, Youngs B, et al. Expression of groups I and II metabotropic glutamate receptors in the rat brain during aging. Brain Res. 2005;1043:95–106
  41. Tanaka S, Nakamura S, Kimura J, Ueda K. Age-related change in the proportion of amyloid precursor protein mRNAs in the gray matter of cerebral cortex. Neurosci Lett. 1993;163:19–21
  42. Han M, Liew CT, Zhang HW, Chao S, Zheng R, Yip KT, et al. Novel blood-based, five-gene biomarker set for the detection of colorectal cancer. Clin Cancer Res. 2008;14:455–460
  43. Twine NC, Stover JA, Marshall B, Dukart G, Hidalgo M, Stadler W, et al. Disease-associated expression profiles in peripheral blood mononuclear cells from patients with advanced renal cell carcinoma. Cancer Res. 2003;63:6069–6075
  44. Osman I, Bajorin DF, Sun TT, Zhong H, Douglas D, Scattergood J, et al. Novel blood biomarkers of human urinary bladder cancer. Clin Cancer Res. 2006;12:3374–3380
  45. Marshall KW, Zhang H, Yager TD, Nossova N, Dempsey A, Zheng R, et al. Blood-based biomarkers for detecting mild osteoarthritis in the human knee. Osteoarthritis Cartilage. 2005;13:861–871
  46. Koczan D, Guthke R, Thiesen HJ, Ibrahim SM, Kundt G, Krentz H, et al. Gene expression profiling of peripheral blood mononuclear leukocytes from psoriasis patients identifies new immune regulatory molecules. Eur J Dermatol. 2005;15:251–257
  47. Nikpour M, Dempsey AA, Urowitz MB, Gladman DD, Barnes DA. Association of a gene expression profile from whole blood with disease activity in systemic lupus erythematosus. Ann Rheum Dis. 2008;67:1069–1075
  48. Burczynski ME, Peterson RL, Twine NC, Zuberek KA, Brodeur BJ, Casciotti L, et al. Molecular classification of Crohn's disease and ulcerative colitis patients using transcriptional profiles in peripheral blood mononuclear cells. J Mol Diagn. 2006;8:51–61
  49. Gregg JP, Lit L, Baron CA, Hertz-Picciotto I, Walker W, Davis RA, et al. Gene expression changes in children with autism. Genomics. 2008;91:22–29
  50. Middleton FA, Pato CN, Gentile KL, McGann L, Brown AM, Trauzzi M, et al. Gene expression analysis of peripheral blood leukocytes from discordant sib-pairs with schizophrenia and bipolar disorder reveals points of convergence between genetic and functional genomic approaches. Am J Med Genet [B] Neuropsychiatr Genet. 2005;136:12–25
  51. Kálmán J, Kitajka K, Pákáski M, Zvara A, Juhász A, Vincze G, et al. Gene expression profile analysis of lymphocytes from Alzheimer's patients. Psychiatr Genet. 2005;15:1–6
  52. Maes OC, Xu S, Yu B, Chertkow HM, Wang E, Schipper HM. Transcriptional profiling of Alzheimer blood mononuclear cells by microarray. Neurobiol Aging. 2007;28:1795–1809
  53. Formichi P, Battisti C, Radi E, Federico A. Cerebrospinal fluid tau, A beta, and phosphorylated tau protein for the diagnosis of Alzheimer's disease. J Cell Physiol. 2006;208:39–46
  54. Bailey P. Biological markers in Alzheimer's disease. Can J Neurol Sci. 2007;34(Suppl 1):S72–S76
  55. Ray S, Britschgi M, Herbert C, Takeda-Uchimura Y, Boxer A, Blennow K, et al. Classification and prediction of clinical Alzheimer's diagnosis based on plasma signaling proteins. Nat Med. 2007;13:1359–1362
  56. Li X, Thyssen G, Beliakoff J, Sun Z. The novel PIAS-like protein hZimp10 enhances Smad transcriptional activity. J Biol Chem. 2006;281:23748–23756
  57. Lee BH, Chen W, Stippec S, Cobb MH. Biological cross-talk between WNK1 and the transforming growth factor beta-Smad signaling pathway. J Biol Chem. 2007;282:17985–17996
  58. Felici A, Wurthner JU, Parks WT, Giam LR, Reiss M, Karpova TS, et al. TLP, a novel modulator of TGF-beta signaling, has opposite effects on Smad2- and Smad3-dependent signaling. EMBO J. 2003;22:4465–4477
  59. Bai RY, Koester C, Ouyang T, Hahn SA, Hammerschmidt M, Peschel C, et al. SMIF, a Smad4-interacting protein that functions as a co-activator in TGFbeta signalling. Nat Cell Biol. 2002;4:181–190
  60. Désiré L, Bourdin J, Loiseau N, Peillon H, Picard V, De Oliveira C, et al. RAC1 inhibition targets amyloid precursor protein processing by gamma-secretase and decreases Abeta production in vitro and in vivo. J Biol Chem. 2005;280:37516–37525
  61. Hoshino M, Sone M, Fukata M, Kuroda S, Kaibuchi K, Nabeshima Y, et al. Identification of the stef gene that encodes a novel guanine nucleotide exchange factor specific for Rac1. J Biol Chem. 1999;274:17837–17844
  62. Heuvingh J, Franco M, Chavrier P, Sykes C. ARF1-mediated actin polymerization produces movement of artificial vesicles. Proc Natl Acad Sci USA. 2007;104:16928–16933
  63. Welch MD, DePace AH, Verma S, Iwamatsu A, Mitchison TJ. The human Arp2/3 complex is composed of evolutionarily conserved subunits and is localized to cellular regions of dynamic actin filament assembly. J Cell Biol. 1997;138:375–384
  64. Kioka N, Sakata S, Kawauchi T, Amachi T, Akiyama SK, Okazaki K, et al. Vinexin: a novel vinculin-binding protein with multiple SH3 domains enhances actin cytoskeletal organization. J Cell Biol. 1999;144:59–69
  65. Hu Y, Leo C, Yu S, Huang BC, Wang H, Shen M, et al. Identification and functional characterization of a novel human misshapen/Nck interacting kinase-related kinase, hMINK beta. J Biol Chem. 2004;279:54387–54397
  66. Zhong Q, Gao W, Du F, Wang X. Mule/ARF-BP1, a BH3-only E3 ubiquitin ligase, catalyzes the polyubiquitination of Mcl-1 and regulates apoptosis. Cell. 2005;121:1085–1095
  67. Tasaki T, Mulder LC, Iwamatsu A, Lee MJ, Davydov IV, Varshavsky A, et al. A family of mammalian E3 ubiquitin ligases that contain the UBR box motif and recognize N-degrons. Mol Cell Biol. 2005;25:7120–7136
  68. Dubiel W, Ferrell K, Pratt G, Rechsteiner M. Subunit 4 of the 26 S protease is a member of a novel eukaryotic ATPase family. J Biol Chem. 1992;267:22699–22702
  69. Davidson JD, Riley B, Burright EN, Duvick LA, Zoghbi HY, Orr HT. Identification and characterization of an ataxin-1-interacting protein: A1Up, a ubiquitin-like nuclear protein. Can Med Assoc J. 2008;178:548–556Hum Mol Genet 2000;9:2305–12

 Conflict of interest: All authors are associated with ExonHit Therapeutics.

PII: S1552-5260(09)02089-5

doi: 10.1016/j.jalz.2009.07.001

Alzheimer's & Dementia: The Journal of the Alzheimer's Association
Volume 6, Issue 1 , Pages 25-38 , January 2010

Article Tools

* Image Usage & Resolution