Differential Network Analyses of Alzheimer's Disease Identify Early Events in Alzheimer's Disease Pathology

International Journal of Alzheimer's Disease

Volumn 2014, Issue , 2015, Pages

  Xia, Jing ^a   Rocke, David M ^b   Perry, George ^c   Ray, Monika ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF TEXAS AT SAN ANTONIO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIPID;

AGED; ALZHEIMER DISEASE; ARTICLE; CONTROLLED STUDY; ENTORHINAL CORTEX; FEMALE; GENE EXPRESSION; HIPPOCAMPUS; HUMAN; LIPID METABOLISM; MALE; MICROARRAY ANALYSIS; MICRODISSECTION; MIDDLE TEMPORAL GYRUS; NERVE CELL; NEUROPATHOLOGY; OXIDATIVE STRESS; POSTERIOR CINGULATE; PRIORITY JOURNAL; SINGLE CELL ANALYSIS;

EID: 84934919006     PISSN: 20908024     EISSN: 20900252     Source Type: Journal    
DOI: 10.1155/2014/721453     Document Type: Article

References (69)

1. W. S. Liang, T. Dunckley, T. G. Beach et al., "Altered neuronal gene expression in brain regions differentially affected by Alzheimer's disease: a reference data set", Physiological Genomics, vol. 33, no. 2, pp. 240-256, 2008.
2. J. Valla, J. D. Berndt, and F. Gonzalez-Lima, "Energy hypometabolism in posterior cingulate cortex of Alzheimer's patients: superficial laminar cytochrome oxidase associated with disease duration", Journal of Neuroscience, vol. 21, no. 13, pp. 4923-4930, 2001.
3. B. A. Vogt, P. B. Crino, and L. J. Vogt, "Reorganization of cingulate cortex in Alzheimer's disease: neuron loss, neuritic plaques, and muscarinic receptor binding", Cerebral Cortex, vol. 2, no. 6, pp. 526-535, 1992.
4. C. Hock, K. Heese, C. Hulette, C. Rosenberg, and U. Otten, "Region-specific neurotrophin imbalances in Alzheimer disease: decreased levels of brain-derived neurotrophic factor and increased levels of nerve growth factor in hippocampus and cortical areas", Archives of Neurology, vol. 57, no. 6, pp. 846-851, 2000.
5. H. Braak and E. Braak, "Evolution of neuronal changes in the course of alzheimer's disease", Journal of Neural Transmission, Supplement, no. 53, pp. 127-140, 1998.
6. H. Braak and E. Braak, "Neuropathological stageing of Alzheimer-related changes", Acta Neuropathologica, vol. 82, no. 4, pp. 239-259, 1991.
7. H. Braak, E. Braak, and J. Bohl, "Staging of Alzheimer-related cortical destruction", European Neurology, vol. 33, no. 6, pp. 403-408, 1993.
8. V. G. Tusher, R. Tibshirani, and G. Chu, "Significance analysis of microarrays applied to the ionizing radiation response", Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 9, pp. 5116-5121, 2001.
9. G. Dennis Jr., B. T. Sherman, D. A. Hosack et al., "DAVID: database for annotation, visualization, and integrated discovery", Genome Biology, vol. 4, no. 5, p. P3, 2003.
10. J. Ruan and W. Zhang, "Identification and evaluation of functional modules in gene co-expression networks", in Proceedings of the RECOMB Satellite Conferences on Systems Biology and Computational Proteomics, pp. 57-76, San Diego, Calif, USA, 2006.
11. M. Ray and W. Zhang, "Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene coexpression networks", BMC Systems Biology, vol. 4, article 136, 2010.
12. M. Ray, R. Yunis, X. Chen, and D. M. Rocke, "Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks", BMC Genomics, vol. 13, no. 1, article 190, 2012.
13. J. E. McDunn, K. D. Husain, A. D. Polpitiya et al., "Plasticity of the systemic inflammatory response to acute infection during critical illness: development of the riboleukogram", PLoS ONE, vol. 3, no. 2, Article ID e1564, 2008.
14. M. Ray, J. Ruan, and W. Zhang, "Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases", Genome Biology, vol. 9, no. 10, article R148, 2008.
15. S. Ekins, Y. Nikolsky, A. Bugrim, E. Kirillov, and T. Nikolskaya, "Pathway mapping tools for analysis of high content data", Methods in Molecular Biology, vol. 356, pp. 319-350, 2007.
16. GeneGo, http://portal.genego.com/help/p-value calculations.pdf.
17. S. Ekins, S. Andreyev, A. Ryabov et al., "A combined approach to drug metabolism and toxicity assessment", Drug Metabolism and Disposition, vol. 34, no. 3, pp. 495-503, 2006.
18. G. Canright and K. Engo-Monsen, "Spreading on networks: a topographic view", in Proceedings of the European Conference on Complex Systems, Paris, France, 2005.
19. P. Bonacich, "Factoring and weighting approaches to status scores and clique identification", Journal of Mathematical Sociology, vol. 2, pp. 113-120, 1972.
20. B. Ruhnau, "Eigenvector-centrality-a node-centrality", Social Networks, vol. 22, no. 4, pp. 357-365, 2000.
21. M. Soler-López, A. Zanzoni, R. Lluís, U. Stelzl, and P. Aloy, "Interactome mapping suggests new mechanistic details underlying Alzheimer's disease", Genome Research, vol. 21, no. 3, pp. 364-376, 2011.
22. A. T. Du, N. Schuff, D. Amend et al., "Magnetic resonance imaging of the entorhinal cortex and hippocampus in mild cognitive impairment and Alzheimer's disease", Journal of Neurology Neurosurgery and Psychiatry, vol. 71, no. 4, pp. 441-447, 2001.
23. M. R. J. Carlson, B. Zhang, Z. Fang, P. S. Mischel, S. Horvath, and S. F. Nelson, "Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks", BMC Genomics, vol. 7, article 40, 2006.
24. M. C. Oldham, S. Horvath, and D. H. Geschwind, "Conservation and evolution of gene coexpression networks in human and chimpanzee brains", Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 47, pp. 17973-17978, 2006.
25. M. C. Oldham, G. Konopka, K. Iwamoto et al., "Functional organization of the transcriptome in human brain", Nature Neuroscience, vol. 11, no. 11, pp. 1271-1282, 2008.
26. H. K. Lee, A. K. Hsu, J. Sajdak, J. Qin, and P. Pavlidis, "Coexpresion analysis of human genes across many microarray data sets", Genome Research, vol. 14, no. 6, pp. 1085-1094, 2004.
27. C. L. Grady, M. L. Furey, P. Pietrini, B. Horwitz, and S. I. Rapoport, "Altered brain functional connectivity and impaired short-term memory in Alzheimer's disease", Brain, vol. 124, no. 4, pp. 739-756, 2001.
28. G. Leuba, A. Savioz, A. Vernay et al., "Differential changes in synaptic proteins in the Alzheimer frontal cortex with marked increase in PSD-95 postsynaptic protein", Journal of Alzheimer's Disease, vol. 15, no. 1, pp. 139-151, 2008.
29. D. E. Bredesen, "Neurodegeneration in Alzheimer's disease: caspases and synaptic element interdependence", Molecular Neurodegeneration, vol. 4, no. 1, article 27, 2009.
30. D. J. Selkoe, "Alzheimer's disease is a synaptic failure", Science, vol. 298, no. 5594, pp. 789-791, 2002.
31. G. J. Ho, R. Drego, E. Hakimian, and E. Masliah, "Mechanisms of cell signaling and inflammation in Alzheimer's disease", Current Drug Targets: Inflammation and Allergy, vol. 4, no. 2, pp. 247-256, 2005.
32. T. Arendt and M. K. Brückner, "Linking cell-cycle dysfunction in alzheimer's disease to a failure of synaptic plasticity", Biochimica et Biophysica Acta, vol. 1772, no. 4, pp. 413-421, 2007.
33. J. Valla, J. D. Berndt, and F. Gonzalez-Lima, "Energy hypometabolism in posterior cingulate cortex of Alzheimer's patients: superficial laminar cytochrome oxidase associated with disease duration", The Journal of Neuroscience, vol. 21, no. 13, pp. 4923-4930, 2001.
34. T.-C. Ho, S.-L. Chen, Y.-C. Yang, C.-L. Liao, H.-C. Cheng, and Y.-P. Tsao, "PEDF induces p53-mediated apoptosis through PPAR gamma signaling in human umbilical vein endothelial cells", Cardiovascular Research, vol. 76, no. 2, pp. 213-223, 2007.
35. T. Yoshida, K. Ohno-Matsui, S. Ichinose et al., "The potential role of amyloid β in the pathogenesis of age-related macular degeneration", Journal of Clinical Investigation, vol. 115, no. 10, pp. 2793-2800, 2005.
36. C. L. Maarouf, I. D. Daugs, T. A. Kokjohn et al., "Alzheimer's disease and non-demented high pathology control nonagenarians: Comparing and contrasting the biochemistry of cognitively successful aging", PLoS ONE, vol. 6, no. 11, Article ID e27291, 2011.
37. P. Cutler, E. L. Akuffo, W. M. Bodnar et al., "Proteomic identification and early validation of complement I inhibitor and pigment epithelium-derived factor: two novel biomarkers of Alzheimer's disease in human plasma", Proteomics: Clinical Applications, vol. 2, no. 4, pp. 467-477, 2008.
38. V. Maletic, M. Robinson, T. Oakes, S. Iyengar, S. G. Ball, and J. Russell, "Neurobiology of depression: an integrated view of key findings", International Journal of Clinical Practice, vol. 61, no. 12, pp. 2030-2040, 2007.
39. P. W. Landfield, E. M. Blalock, K. Chen, and N. M. Porter, "A new glucocorticoid hypothesis of brain aging: implications for Alzheimer's disease", Current Alzheimer Research, vol. 4, no. 2, pp. 205-212, 2007.
40. W. Li, Y. Yao, W. Zhang, Y. Yin, G. Wu, and H. Gong, "Glucocorticoids increase impairments in learning and memory due to elevated amyloid precursor protein expression and neuronal apoptosis in 12-month old mice", European Journal of Pharmacology, vol. 628, no. 1-3, pp. 108-115, 2010.
41. R. A. C. M. Boonen, P. Van Tijn, and D. Zivkovic, "Wnt signaling in Alzheimer's disease: up or down, that is the question", Ageing Research Reviews, vol. 8, no. 2, pp. 71-82, 2009.
42. N. C. Inestrosa, L. Varela-Nallar, C. P. Grabowski, and M. Colombres, "Synaptotoxicity in Alzheimer's disease: the Wnt signaling pathway as a molecular target", IUBMB Life, vol. 59, no. 4-5, pp. 316-321, 2007.
43. G. V. De Ferrari, A. Papassotiropoulos, T. Biechele et al., "Common genetic variation within the low-density lipoprotein receptor-related protein 6 and late-onset alzheimer's disease", Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 22, pp. 9434-9439, 2007.
44. K. Herrup, "The involvement of cell cycle events in the pathogenesis of Alzheimer's disease", Alzheimer's Research and Therapy, vol. 2, no. 3, article 13, 2010.
45. J. P. Lopes, C. R. Oliveira, and P. Agostinho, "Cell cycle re-entry in Alzheimer's disease: a major neuropathological characteristic?" Current Alzheimer Research, vol. 6, no. 3, pp. 205-212, 2009.
46. D. J. Bonda, H. Lee, W. Kudo, X. Zhu, and M. A. Smith, "Pathological implications of cell cycle re-entry in Alzheimer disease", Expert Reviews in Molecular Medicine, vol. 12, article e19, 2010.
47. R. Gerlai, "EphB and NMDA receptors: components of synaptic plasticity coming together", Trends in Neurosciences, vol. 25, no. 4, pp. 180-181, 2002.
48. R. Dufault, R. Schnoll, W. J. Lukiw et al., "Mercury exposure, nutritional deficiencies and metabolic disruptions may affect learning in children", Behavioral and Brain Functions, vol. 5, article 44, 2009.
49. D. Costantini, V. Marasco, and A. P. Møller, "A meta-analysis of glucocorticoids asmodulators of oxidative stress in vertebrates", Journal of Comparative Physiology B, vol. 181, no. 4, pp. 447-456, 2011.
50. T. A. Evans, A. K. Raina, A. Delacourte et al., "BRCA1 may modulate neuronal cell cycle re-entry in Alzheimer disease", International Journal of Medical Sciences, vol. 4, no. 3, pp. 140-145, 2007.
51. G. Perry, A. D. Cash, and M. A. Smith, "Alzheimer disease and oxidative stress", Journal of Biomedicine and Biotechnology, vol. 2, no. 3, pp. 120-123, 2002.
52. R. J. Castellani, P. I. Moreira, G. Liu et al., "Iron: the redox-active center of oxidative stress in Alzheimer disease", Neurochemical Research, vol. 32, no. 10, pp. 1640-1645, 2007.
53. S. Gandhi and A. Y. Abramov, "Mechanismof oxidative stress in neurodegeneration", OxidativeMedicine and Cellular Longevity, vol. 2012, Article ID 428010, 11 pages, 2012.
54. T. Murakami, Y. Moriwaki, T. Kawarabayashi et al., "PINK1, a gene product of PARK6, accumulates in α-synucleinopathy brains", Journal of Neurology, Neurosurgery and Psychiatry, vol. 78, no. 6, pp. 653-655, 2007.
55. Y. Hatano, K. Sato, B. Elibol et al., "PARK6-linked autosomal recessive early-onset parkinsonism in Asian populations", Neurology, vol. 63, no. 8, pp. 1482-1485, 2004.
56. N. Matsuda, S. Sato, K. Shiba et al., "PINK1 stabilized by mitochondrial depolarization recruits Parkin to damaged mitochondria and activates latent Parkin for mitophagy", Journal of Cell Biology, vol. 189, no. 2, pp. 211-221, 2010.
57. K. Goh, M. E. Cusick, D. Valle, B. Childs, M. Vidal, and A. Barabási, "The human disease network", Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 21, pp. 8685-8690, 2007.
58. S. Greenblum, P. J. Turnbaugh, and E. Borenstein, "Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease", Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 2, pp. 594-599, 2012.
59. F. Barrenas, S. Chavali, P. Holme, R. Mobini, and M. Benson, "Network properties of complex human disease genes identified through genome-wide association studies", PLoS ONE, vol. 4, no. 11, Article ID e0008090, 2009.
60. W. De Haan, W. M. Van Der Flier, H. Wang, P. F. Van Mieghem, P. Scheltens, and C. J. Stam, "Disruption of functional brain networks in alzheimer's disease: what can we learn from graph spectral analysis of resting-state magnetoencephalography?" Brain Connection, vol. 2, no. 2, pp. 45-55, 2012.
61. X. Zhao, Y. Liu, X. Wang et al., "Disrupted small-world brain networks in moderate Alzheimer's disease: a resting-state fMRI study", PLoS ONE, vol. 7, no. 3, Article ID e33540, 2012.
62. Y. He, Z. Chen, and A. Evans, "Structural insights into aberrant topological patterns of large-scale cortical networks in Alzheimer's disease", Journal of Neuroscience, vol. 28, no. 18, pp. 4756-4766, 2008.
63. M. J. Stampfer, "Cardiovascular disease and Alzheimer's disease: common links", Journal of InternalMedicine, vol. 260, no. 3, pp. 211-223, 2006.
64. C. Rosendorff, M. S. Beeri, and J. M. Silverman, "Cardiovascular risk factors for Alzheimer's disease", American Journal of Geriatric Cardiology, vol. 16, no. 3, pp. 143-149, 2007.
65. R. Stewart, "Cardiovascular factors in Alzheimer's disease", Journal of Neurology Neurosurgery and Psychiatry, vol. 65, no. 2, pp. 143-147, 1998.
66. J. Janson, T. Laedtke, J. E. Parisi, P. O'Brien, R. C. Petersen, and P. C. Butler, "Increased risk of type 2 diabetes in alzheimer disease", Diabetes, vol. 53, no. 2, pp. 474-481, 2004.
67. C. MacKnight, K. Rockwood, E. Awalt, and I. McDowell, "Diabetesmellitus and the risk of dementia, Alzheimer's disease and vascular cognitive impairment in the Canadian Study of Health and Aging", Dementia and Geriatric Cognitive Disorders, vol. 14, no. 2, pp. 77-83, 2002.
68. S. Craft and G. S. Watson, "Insulin and neurodegenerative disease: shared and specificmechanisms", The Lancet Neurology, vol. 3, no. 3, pp. 169-178, 2004.
69. F. Billia, L. Hauck, F. Konecny, V. Rao, J. Shen, and T. W. Mak, "PTEN-inducible kinase 1 (PINK1)/Park6 is indispensable for normal heart function", Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 23, pp. 9572-9577, 2011