Molecular network of microRNA targets in Alzheimer's disease brains

Experimental Neurology

Volumn 235, Issue 2, 2012, Pages 436-446

  Satoh, Jun ichi ^a  

^a MEIJI PHARMACEUTICAL UNIVERSITY   (Japan)

Author keywords

Alzheimer's disease; Cell cycle; KEGG; KeyMolnet; MicroRNA; MiRTarBase

Indexed keywords

AMYLOID BETA PROTEIN; MICRORNA;

ALZHEIMER DISEASE; APOPTOSIS; BIOINFORMATICS; CELL CYCLE PROGRESSION; CELL CYCLE REGULATION; CELL METABOLISM; CELL PROLIFERATION; GENE EXPRESSION REGULATION; GENE REPRESSION; GENE TARGETING; HUMAN; NERVE CELL DIFFERENTIATION; NEUROFIBRILLARY TANGLE; NEUROPATHOLOGY; NONHUMAN; PARKINSON DISEASE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RNA ANALYSIS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION;

ALZHEIMER DISEASE; ANIMALS; BRAIN; BRAIN CHEMISTRY; GENE REGULATORY NETWORKS; GENE TARGETING; HUMANS; MICRORNAS;

EID: 84858269210     PISSN: 00144886     EISSN: 10902430     Source Type: Journal    
DOI: 10.1016/j.expneurol.2011.09.003     Document Type: Review

References (49)

1. Albert R., Jeong H., Barabasi A.L. Error and attack tolerance of complex networks. Nature 2000, 406:378-382.
2. Bettens K., Brouwers N., Engelborghs S., Van Miegroet H., De Deyn P.P., Theuns J., Sleegers K., Van Broeckhoven C. APP and BACE1 miRNA genetic variability has no major role in risk for Alzheimer disease. Hum. Mutat. 2009, 30:1207-1213.
3. Boissonneault V., Plante I., Rivest S., Provost P. MicroRNA-298 and microRNA-328 regulate expression of mouse β-amyloid precursor protein-converting enzyme 1. J. Biol. Chem. 2009, 284:1971-1981.
4. Bonda D.J., Lee H.P., Kudo W., Zhu X., Smith M.A., Lee H.G. Pathological implications of cell cycle re-entry in Alzheimer disease. Expert Rev. Mol. Med. 2010, 12:e19.
5. Busser J., Geldmacher D.S., Herrup K. Ectopic cell cycle proteins predict the sites of neuronal cell death in Alzheimer's disease brain. J. Neurosci. 1998, 18:2801-2807.
6. Cogswell J.P., Ward J., Taylor I.A., Waters M., Shi Y., Cannon B., Kelnar K., Kemppainen J., Brown D., Chen C., Prinjha R.K., Richardson J.C., Saunders A.M., Roses A.D., Richards C.A. Identification of miRNA changes in Alzheimer's disease brain and CSF yields putative biomarkers and insights into disease pathways. J. Alzheimers Dis. 2008, 14:27-41.
7. Cui J.G., Li Y.Y., Zhao Y., Bhattacharjee S., Lukiw W.J. Differential regulation of interleukin-1 receptor-associated kinase-1 (IRAK-1) and IRAK-2 by microRNA-146a and NF-κB in stressed human astroglial cells and in Alzheimer disease. J. Biol. Chem. 2010, 285:38951-38960.
8. Faghihi M.A., Modarresi F., Khalil A.M., Wood D.E., Sahagan B.G., Morgan T.E., Finch C.E., St Laurent G., Kenny P.J., Wahlestedt C. Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase. Nat. Med. 2008, 14:723-730.
9. Faghihi M.A., Zhang M., Huang J., Modarresi F., Van der Brug M.P., Nalls M.A., Cookson M.R., St-Laurent G., Wahlestedt C. Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol. 2010, 11:R56.
10. Filipowicz W., Bhattacharyya S.N., Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?. Nat. Rev. Genet. 2008, 9:102-114.
11. Fineberg S.K., Kosik K.S., Davidson B.L. MicroRNAs potentiate neural development. Neuron 2009, 64:303-309.
12. Friedman R.C., Farh K.K., Burge C.B., Bartel D.P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009, 19:92-105.
13. Harraz M.M., Dawson T.M., Dawson V.L. MicroRNAs in Parkinson's disease. J. Chem. Neuroanat. 2011, 42:127-130.
14. Hébert S.S., Horré K., Nicolaï L., Papadopoulou A.S., Mandemakers W., Silahtaroglu A.N., Kauppinen S., Delacourte A., De Strooper B. Loss of microRNA cluster miR-29a/b-1 in sporadic Alzheimer's disease correlates with increased BACE1/beta-secretase expression. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:6415-6420.
15. Hébert S.S., Horré K., Nicolaï L., Bergmans B., Papadopoulou A.S., Delacourte A., De Strooper B. MicroRNA regulation of Alzheimer's amyloid precursor protein expression. Neurobiol. Dis. 2009, 33:422-428.
16. Hébert S.S., Papadopoulou A.S., Smith P., Galas M.C., Planel E., Silahtaroglu A.N., Sergeant N., Buée L., De Strooper B. Genetic ablation of Dicer in adult forebrain neurons results in abnormal tau hyperphosphorylation and neurodegeneration. Hum. Mol. Genet. 2010, 19:3959-3969.
17. Hsu C.W., Juan H.F., Huang H.C. Characterization of microRNA-regulated protein-protein interaction network. Proteomics 2008, 8:1975-1979.
18. Hsu S.D., Lin F.M., Wu W.Y., Liang C., Huang W.C., Chan W.L., Tsai W.T., Chen G.Z., Lee C.J., Chiu C.M., Chien C.H., Wu M.C., Huang C.Y., Tsou A.P., Huang H.D. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res. 2011, 39:D163-D169.
19. Huang da W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
20. Kanehisa M., Goto S., Furumichi M., Tanabe M., Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 2010, 38:D355-D360.
21. Kitano H. A robustness-based approach to systems-oriented drug design. Nat. Rev. Drug Discov. 2007, 6:202-210.
22. Kocerha J., Kauppinen S., Wahlestedt C. microRNAs in CNS disorders. Neuromolecular Med. 2009, 11:162-172.
23. Lukiw W.J. Micro-RNA speciation in fetal, adult and Alzheimer's disease hippocampus. Neuroreport 2007, 18:297-300.
24. Lukiw W.J., Zhao Y., Cui J.G. An NF-κB-sensitive micro RNA-146a-mediated inflammatory circuit in Alzheimer disease and in stressed human brain cells. J. Biol. Chem. 2008, 283:31315-31322.
25. Maes T., Barceló A., Buesa C. Neuron navigator: a human gene family with homology to unc-53, a cell guidance gene from Caenorhabditis elegans. Genomics 2002, 80:21-30.
26. Maes O.C., Chertkow H.M., Wang E., Schipper H.M. MicroRNA: implications for Alzheimer disease and other human CNS disorders. Curr. Genomics 2009, 10:154-168.
27. McShea A., Harris P.L., Webster K.R., Wahl A.F., Smith M.A. Abnormal expression of the cell cycle regulators P16 and CDK4 in Alzheimer's disease. Am. J. Pathol. 1997, 150:1933-1939.
28. Mitchell P.S., Parkin R.K., Kroh E.M., Fritz B.R., Wyman S.K., Pogosova-Agadjanyan E.L., Peterson A., Noteboom J., O'Briant K.C., Allen A., Lin D.W., Urban N., Drescher C.W., Knudsen B.S., Stirewalt D.L., Gentleman R., Vessella R.L., Nelson P.S., Martin D.B., Tewari M. Circulating microRNAs as stable blood-based markers for cancer detection. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:10513-10518.
29. Nelson P.T., Wang W.X. MiR-107 is reduced in Alzheimer's disease brain neocortex: validation study. J. Alzheimers Dis. 2010, 21:75-79.
30. Nelson P.T., Wang W.X., Rajeev B.W. MicroRNAs (miRNAs) in neurodegenerative diseases. Brain Pathol. 2008, 18:130-138.
31. Nelson P.T., Dimayuga J., Wilfred B.R. MicroRNA in situ hybridization in the human entorhinal and transentorhinal cortex. Front. Hum. Neurosci. 2010, 4:7.
32. Nunez-Iglesias J., Liu C.C., Morgan T.E., Finch C.E., Zhou X.J. Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals altered miRNA regulation. PLoS One 2010, 5:e8898.
33. Ranganathan S., Scudiere S., Bowser R. Hyperphosphorylation of the retinoblastoma gene product and altered subcellular distribution of E2F-1 during Alzheimer's disease and amyotrophic lateral sclerosis. J. Alzheimers Dis. 2001, 3:377-385.
34. Satoh J. MicroRNAs and their therapeutic potential for human diseases: aberrant microRNA expression in Alzheimer's disease brains. J. Pharmacol. Sci. 2010, 114:269-275.
35. Satoh J., Tabunoki H. Comprehensive analysis of human microRNA target networks. BioData Min. 2011, 4:17.
36. Satoh J., Tabunoki H., Arima K. Molecular network analysis suggests aberrant CREB-mediated gene regulation in the Alzheimer disease hippocampus. Dis. Markers 2009, 27:239-252.
37. Schratt G.M., Tuebing F., Nigh E.A., Kane C.G., Sabatini M.E., Kiebler M., Greenberg M.E. A brain-specific microRNA regulates dendritic spine development. Nature 2006, 439:283-289.
38. Selbach M., Schwanhäusser B., Thierfelder N., Fang Z., Khanin R., Rajewsky N. Widespread changes in protein synthesis induced by microRNAs. Nature 2008, 455:58-63.
39. Sethi P., Lukiw W.J. Micro-RNA abundance and stability in human brain: specific alterations in Alzheimer's disease temporal lobe neocortex. Neurosci. Lett. 2009, 459:100-104.
40. Shioya M., Obayashi S., Tabunoki H., Arima K., Saito Y., Ishida T., Satoh J. Aberrant microRNA expression in the brains of neurodegenerative diseases: miR-29a decreased in Alzheimer disease brains targets neuron navigator-3. Neuropathol. Appl. Neurobiol. 2010, 36:320-330.
41. Smith P., Al Hashimi A., Girard J., Delay C., Hébert S.S. In vivo regulation of amyloid precursor protein neuronal splicing by microRNAs. J. Neurochem. 2011, 116:240-247.
42. Swiss V.A., Casaccia P. Cell-context specific role of the E2F/Rb pathway in development and disease. Glia 2010, 58:377-390.
43. Vasudevan S., Tong Y., Steitz J.A. Switching from repression to activation: microRNAs can up-regulate translation. Science 2007, 318:1931-1934.
44. Vilardo E., Barbato C., Ciotti M., Cogoni C., Ruberti F. MicroRNA-101 regulates amyloid precursor protein expression in hippocampal neurons. J. Biol. Chem. 2010, 285:18344-18351.
45. Viswanathan G.A., Seto J., Patil S., Nudelman G., Sealfon S.C. Getting started in biological pathway construction and analysis. PLoS Comput. Biol. 2008, 4:e16.
46. Wang W.X., Rajeev B.W., Stromberg A.J., Ren N., Tang G., Huang Q., Rigoutsos I., Nelson P.T. The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of β-site amyloid precursor protein-cleaving enzyme 1. J. Neurosci. 2008, 28:1213-1223.
47. Wang W.X., Huang Q., Hu Y., Stromberg A.J., Nelson P.T. Patterns of microRNA expression in normal and early Alzheimer's disease human temporal cortex: white matter versus gray matter. Acta Neuropathol. 2011, 121:193-205.
48. Yang Y., Mufson E.J., Herrup K. Neuronal cell death is preceded by cell cycle events at all stages of Alzheimer's disease. J. Neurosci. 2003, 23:2557-2563.
49. Yao J., Hennessey T., Flynt A., Lai E., Beal M.F., Lin M.T. MicroRNA-related cofilin abnormality in Alzheimer's disease. PLoS One 2010, 5:e15546.