The central role of AMP-kinase and energy homeostasis impairment in Alzheimer's disease: A multifactor network analysis

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Caberlotto, Laura ^a   Lauria, Mario ^a   Nguyen, Thanh Phuong ^a   Scotti, Marco ^a  

^a UNIVERSITY OF TRENTO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLATE KINASE;

ALZHEIMER DISEASE; ARTICLE; AUTOPHAGY; CLINICAL ARTICLE; CONTROLLED STUDY; DRUG TARGETING; ENZYME ACTIVATION; ENZYME ACTIVITY; GENE; GENE EXPRESSION; GENETIC ASSOCIATION; HOMEOSTASIS; HUMAN; NEUROPATHOLOGY; PROTEIN PROTEIN INTERACTION; SEED GENE; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM;

ALZHEIMER DISEASE; AMP-ACTIVATED PROTEIN KINASES; CLUSTER ANALYSIS; ENERGY METABOLISM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HOMEOSTASIS; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; SIGNAL TRANSDUCTION;

EID: 84893386226     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0078919     Document Type: Article

References (55)

1. Huang Y, Mucke L (2012) Alzheimer mechanisms and therapeutic strategies. Cell 148: 1204-1222.
2. Bertram L, Tanzi RE (2008) Thirty years of Alzheimer's disease genetics: the implications of systematic meta-analyses. Nature reviews Neuroscience 9: 768-778.
3. Citron M (2010) Alzheimer's disease: strategies for disease modification. Nature reviews Drug discovery 9: 387-398.
4. Butler AW, Ng MYM, Hamshere ML, Forabosco P, Wroe R, et al. (2009) Metaanalysis of linkage studies for Alzheimer's disease-a web resource. Neurobiology of aging 30: 1037-1047.
5. Bertram L, Lill CM, Tanzi RE (2010) The genetics of Alzheimer disease: back to the future. Neuron 68: 270-281.
6. Guttula SV, Allam A, Gumpeny RS (2012) Analyzing microarray data of Alzheimer's using cluster analysis to identify the biomarker genes. International journal of Alzheimer's disease 2012: 649456.
7. Emilsson L, Saetre P, Jazin E (2006) Alzheimer's disease: mRNA expression profiles of multiple patients show alterations of genes involved with calcium signaling. Neurobiology of disease 21: 618-625. (Pubitemid 43277543)
8. Katsel P, Li C, Haroutunian V (2007) Gene expression alterations in the sphingolipid metabolism pathways during progression of dementia and Alzheimer's disease: a shift toward ceramide accumulation at the earliest recognizable stages of Alzheimer's disease? Neurochemical research 32: 845-856. (Pubitemid 46481322)
9. Bossers K, Wirz KTS, Meerhoff GF, Essing AHW, Van Dongen JW, et al. (2010) Concerted changes in transcripts in the prefrontal cortex precede neuropathology in Alzheimer's disease. Brain: a journal of neurology 133: 3699-3723.
10. Sun J, Feng X, Liang D, Duan Y, Lei H (2012) Down-regulation of energy metabolism in Alzheimer's disease is a protective response of neurons to the microenvironment. Journal of Alzheimer's disease: JAD 28: 389-402.
11. Liang WS, Reiman EM, Valla J, Dunckley T, Beach TG, et al. (2008) Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons. Proceedings of the National Academy of Sciences of the United States of America 105: 4441-4446. (Pubitemid 351754399)
12. Krauthammer M, Kaufmann CA, Gilliam TC, Rzhetsky A (2004) Molecular triangulation: Bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. 101: 15148-15153.
13. Chen JY, Shen C, Sivachenko AY (2006) Mining Alzheimer disease relevant proteins from integrated protein interactome data. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing: 367-378. Available.
14. Liu B, Jiang T, Ma S, Zhao H, Li J, et al. (2006) Exploring candidate genes for human brain diseases from a brain-specific gene network. Biochemical and biophysical research communications 349: 1308-1314. (Pubitemid 44416400)
15. Soler-López M, Zanzoni A, Lluís R, Stelzl U, Aloy P, et al. (2011) Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. Genome research 21: 364-376.
16. Lauria M (2013) Rank-based transcriptional signatures: a novel approach to diagnostic biomarker definition and analysis. Systems Biomedicine in press.
17. Bertram L, McQueen MB, Mullin K, Blacker D TR (2007) Systematic metaanalyses of Alzheimer disease genetic association studies: the AlzGene. Nat Genet 39: 17-23. (Pubitemid 46026496)
18. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic acids research 33: D514-7. (Pubitemid 40207927)
19. Calvano SE, Xiao W, Richards DR, Felciano RM, Baker H V, et al. (2005) A network-based analysis of systemic inflammation in humans. Nature 437: 1032-1037. (Pubitemid 41486985)
20. Komurov K, Dursun S, Erdin S, Ram PT (2012) NetWalker: a contextual network analysis tool for functional genomics. BMC genomics 13: 282.
21. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database-2009 update. Nucleic acids research 37: D767-72.
22. Tarca AL, Lauria M, Unger M, Bilal E, Boue S, et al. (2013) Strengths and limitations of microarray-based phenotype prediction: Lessons learned from the IMPROVER Diagnostic Signature Challenge. Bioinformatics (Oxford, England).
23. Reichardt J, Bornholdt S (2006) Statistical mechanics of community detection. Physical review E, Statistical, nonlinear, and soft matter physics 74: 016110.
24. G Csardi, Nepusz T (2006) The igraph software package for complex network research. IntJCompSyst 1695.
25. Newman MEJ, Girvan M (2004) Finding and evaluating community structure in networks. Physical review E, Statistical, nonlinear, and soft matter physics 69: 026113.
26. Wang X, Terfve C, Rose JC, Markowetz F (2011) HTSanalyzeR: an R/ Bioconductor package for integrated network analysis of high-throughput screens. Bioinformatics (Oxford, England) 27: 879-880.
27. Sturges HA (1926) The choice of a class interval. Journal of the American Statistical Association 21: 65-66.
28. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC bioinformatics 10: 48.
29. Supek F, Bošnjak M, Škunca N, Šmuc T (2011) REVIGO summarizes and visualizes long lists of gene ontology terms. PloS one 6: e21800.
30. Benjamini Y., Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series 57: 289-300.
31. Murdoch D, Tsai Y AJ (2008) P-Values are Random Variables. The American Statistician 62: 242-245.
32. Rice J R (1995) Mathematical statistics and data analysis. Belmont: Duxbury Press: 594.
33. Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics (Oxford, England) 24: i223-31. (Pubitemid 351911677)
34. Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL, Shen EH, Ng L, et al. (2012) An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489: 391-399.
35. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 102: 15545-15550. (Pubitemid 41528093)
36. Ackermann M, Strimmer K (2009) A general modular framework for gene set enrichment analysis. BMC bioinformatics 10: 47.
37. Minoshima S, Giordani B, Berent S, Frey KA, Foster NL, et al. (1997) Metabolic reduction in the posterior cingulate cortex in very early Alzheimer's disease. Annals of neurology 42: 85-94. (Pubitemid 27304784)
38. Ahmad W (2013) Overlapped metabolic and therapeutic links between Alzheimer and diabetes. Molecular neurobiology 47: 399-424.
39. Piaceri I, Rinnoci V, Bagnoli S, Failli Y, Sorbi S (2012) Mitochondria and Alzheimer's disease. Journal of the neurological sciences 322: 31-34.
40. Moreira PI, Santos RX, Zhu X, Lee H, Smith MA, et al. (2010) Autophagy in Alzheimer's disease. Expert review of neurotherapeutics 10: 1209-1218.
41. Mairet-Coello G, Courchet J, Pieraut S, Courchet V, Maximov A, et al. (2013) The CAMKK2-AMPK Kinase Pathway Mediates the Synaptotoxic Effects of Ab Oligomers through Tau Phosphorylation. Neuron 78: 94-108.
42. Van Someren EJ, Mirmiran M, Swaab DF (1993) Non-pharmacological treatment of sleep and wake disturbances in aging and Alzheimer's disease: chronobiological perspectives. Behavioural brain research 57: 235-253. (Pubitemid 24027154)
43. Valentin F, Squizzato S, Goujon M, McWilliam H, Paern J, et al. (2010) Fast and efficient searching of biological data resources-using EB-eye. Briefings in bioinformatics 11: 375-384.
44. Searcy JL, Phelps JT, Pancani T, Kadish I, Popovic J, et al. (2012) Long-term pioglitazone treatment improves learning and attenuates pathological markers in a mouse model of Alzheimer's disease. Journal of Alzheimer's disease: JAD 30: 943-961.
45. Jiang Q, Heneka M, Landreth GE (2008) The role of peroxisome proliferatoractivated receptor-gamma (PPARgamma) in Alzheimer's disease: therapeutic implications. CNS drugs 22: 1-14. (Pubitemid 350243363)
46. Lin A, Wang RT, Ahn S, Park CC, Smith DJ (2010) A genome-wide map of human genetic interactions inferred from radiation hybrid genotypes. Genome research 20: 1122-1132.
47. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, et al. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science (New York, NY) 302: 2141-2144. (Pubitemid 38017950)
48. Greco SJ, Sarkar S, Johnston JM, Tezapsidis N (2009) Leptin regulates tau phosphorylation and amyloid through AMPK in neuronal cells. Biochemical and biophysical research communications 380: 98-104.
49. Mizuno S, Iijima R, Ogishima S, Kikuchi M, Matsuoka Y, et al. (2012) AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease. BMC systems biology 6: 52.
50. Nelson PT, Alafuzoff I, Bigio EH, Bouras C, Braak H, et al. (2012) Correlation of Alzheimer disease neuropathologic changes with cognitive status: a review of the literature. Journal of neuropathology and experimental neurology 71: 362-381.
51. Minokoshi Y, Alquier T, Furukawa N, Kim Y-B, Lee A, et al. (2004) AMPkinase regulates food intake by responding to hormonal and nutrient signals in the hypothalamus. Nature 428: 569-574. (Pubitemid 38480541)
52. Potter WB, O'Riordan KJ, Barnett D, Osting SMK, Wagoner M, et al. (2010) Metabolic regulation of neuronal plasticity by the energy sensor AMPK. PloS one 5: e8996.
53. Cai Z, Yan L-J, Li K, Quazi SH, Zhao B (2012) Roles of AMP-activated protein kinase in Alzheimer's disease. Neuromolecular medicine 14: 1-14.
54. Cai H, Cong W, Ji S, Rothman S, Maudsley S, et al. (2012) Metabolic dysfunction in Alzheimer's disease and related neurodegenerative disorders. Current Alzheimer research 9: 5-17.
55. Salminen A, Kaarniranta K (2012) AMP-activated protein kinase (AMPK) controls the aging process via an integrated signaling network. Ageing research reviews 11: 230-241.