Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2015 (2015), Article ID 394260, 13 pages
http://dx.doi.org/10.1155/2015/394260
Research Article

The Construction of Common and Specific Significance Subnetworks of Alzheimer’s Disease from Multiple Brain Regions

1Information Engineering College, Shanghai Maritime University, Shanghai 201306, China
2DNJ Pharma and Rowan University, Glassboro, NJ 08028, USA
3Psychology Department, The Second People’s Hospital of Guizhou Province, Guiyang 550004, China
4Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China

Received 28 August 2014; Accepted 7 October 2014

Academic Editor: Tao Huang

Copyright © 2015 Wei Kong et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. M. Meyer-Luehmann, T. L. Spires-Jones, C. Prada et al., “Rapid appearance and local toxicity of amyloid-β plaques in a mouse model of Alzheimer's disease,” Nature, vol. 451, no. 7179, pp. 720–725, 2008. View at Publisher · View at Google Scholar · View at Scopus
  2. P. D. Wes, A. Easton, J. Corradi et al., “Tau overexpression impacts a neuroinflammation gene expression network perturbed in Alzheimer's disease,” PLoS ONE, vol. 9, no. 8, Article ID e106050, 2014. View at Publisher · View at Google Scholar
  3. 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. View at Publisher · View at Google Scholar · View at Scopus
  4. J. F. Loring, X. Wen, J. M. Lee, J. Seilhamer, and R. Somogyi, “A gene expression profile of Alzheimer's disease,” DNA and Cell Biology, vol. 20, no. 11, pp. 683–695, 2001. View at Publisher · View at Google Scholar · View at Scopus
  5. T. Dunckley, T. G. Beach, K. E. Ramsey et al., “Gene expression correlates of neurofibrillary tangles in Alzheimer's disease,” Neurobiology of Aging, vol. 27, no. 10, pp. 1359–1371, 2006. View at Publisher · View at Google Scholar · View at Scopus
  6. 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. View at Publisher · View at Google Scholar · View at Scopus
  7. 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. View at Publisher · View at Google Scholar · View at Scopus
  8. J. A. Miller, M. C. Oldham, and D. H. Geschwind, “A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging,” The Journal of Neuroscience, vol. 28, no. 6, pp. 1410–1420, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. M. Ray and W. Zhang, “Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks,” BMC Systems Biology, vol. 4, article 136, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. Z.-P. Liu, Y. Wang, X.-S. Zhang, and L. Chen, “Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains,” BMC Systems Biology, vol. 4, no. 2, article 11, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. Z.-P. Liu, Y. Wang, X.-S. Zhang, W. Xia, and L. Chen, “Detecting and analyzing differentially activated pathways in brain regions of Alzheimer's disease patients,” Molecular BioSystems, vol. 7, no. 5, pp. 1441–1452, 2011. View at Publisher · View at Google Scholar · View at Scopus
  12. D. Liang, G. Han, X. Feng, J. Sun, Y. Duan, and H. Lei, “Concerted perturbation observed in a hub network in Alzheimer's disease,” PLoS ONE, vol. 7, no. 7, Article ID e40498, 2012. View at Publisher · View at Google Scholar · View at Scopus
  13. F. Chen, Q. Guan, Z.-Y. Nie, and L.-J. Jin, “Gene expression profile and functional analysis of Alzheimer's disease,” American Journal of Alzheimer's Disease and other Dementias, vol. 28, no. 7, pp. 693–701, 2013. View at Publisher · View at Google Scholar · View at Scopus
  14. Z. Guo, L. Wang, Y. Li et al., “Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network,” Bioinformatics, vol. 23, no. 16, pp. 2121–2128, 2007. View at Google Scholar
  15. M. T. Dittrich, G. W. Klau, A. Rosenwald, T. Dandekar, and T. Müller, “Identifying functional modules in protein-protein interaction networks: an integrated exact approach,” Bioinformatics, vol. 24, no. 13, pp. i223–i231, 2008. View at Publisher · View at Google Scholar · View at Scopus
  16. D. W. Ding, P. Yang, and X. H. Wu, “Application of simulated annealing algorithm to biological network research,” Computers and Applied Chemistry, vol. 28, no. 10, pp. W1302–W1304, 2011. View at Google Scholar
  17. W. E. Müller, A. Eckert, C. Kurz, G. P. Eckert, and K. Leuner, “Mitochondrial dysfunction: common final pathway in brain aging and alzheimer's disease-therapeutic aspects,” Molecular Neurobiology, vol. 41, no. 2-3, pp. 159–171, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. D. W. Huang, B. T. Sherman, and R. A. Lempicki, “Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources,” Nature Protocols, vol. 4, no. 1, pp. 44–57, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. H. Akiyama, S. Barger, S. Barnum et al., “Inflammation and Alzheimer's disease,” Neurobiology of Aging, vol. 21, no. 3, pp. 383–421, 2000. View at Google Scholar
  20. J. A. McCubrey, M. M. Lahair, and R. A. Franklin, “Reactive oxygen species-induced activation of the MAP kinase signaling pathways,” Antioxidants & Redox Signaling, vol. 8, no. 9-10, pp. 1775–1789, 2006. View at Google Scholar
  21. S. Torii, T. Yamamoto, Y. Tsuchiya, and E. Nishida, “ERK MAP kinase in G1 cell cycle progression and cancer,” Cancer Science, vol. 97, no. 8, pp. 697–702, 2006. View at Publisher · View at Google Scholar · View at Scopus
  22. A. S. Dhillon, S. Hagan, O. Rath, and W. Kolch, “MAP kinase signalling pathways in cancer,” Oncogene, vol. 26, no. 22, pp. 3279–3290, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. E. K. Kim and E.-J. Choi, “Pathological roles of MAPK signaling pathways in human diseases,” Biochimica et Biophysica Acta—Molecular Basis of Disease, vol. 1802, no. 4, pp. 396–405, 2010. View at Publisher · View at Google Scholar · View at Scopus
  24. E. S. Alnemri, D. J. Livingston, D. W. Nicholson et al., “Human ICE/CED-3 protease nomenclature,” Cell, vol. 87, no. 2, p. 171, 1996. View at Publisher · View at Google Scholar · View at Scopus
  25. D. R. McIlwain, T. Berger, and T. W. Mak, “Caspase functions in cell death and disease,” Cold Spring Harbor Perspectives in Biology, vol. 5, no. 4, Article ID a008656, 2013. View at Publisher · View at Google Scholar · View at Scopus
  26. N. Bulat and C. Widmann, “Caspase substrates and neurodegenerative diseases,” Brain Research Bulletin, vol. 80, no. 4-5, pp. 251–267, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. M. J. Chong, M. R. Murray, E. C. Gosink et al., “Atm and Bax cooperate in ionizing radiation-induced apoptosis in the central nervous system,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 2, pp. 889–894, 2000. View at Publisher · View at Google Scholar · View at Scopus
  28. T. Uetsuki, K. Takemoto, I. Nishimura et al., “Activation of neuronal caspase-3 by intracellular accumulation of wild- type Alzheimer amyloid precursor protein,” Journal of Neuroscience, vol. 19, no. 16, pp. 6955–6964, 1999. View at Google Scholar · View at Scopus
  29. D. L. Krebs and D. J. Hilton, “SOCS: physiological suppressors of cytokine signaling,” Journal of Cell Science, vol. 113, part 16, pp. 2813–2819, 2000. View at Google Scholar · View at Scopus
  30. Y. Lu, S. Fukuyama, R. Yoshida et al., “Loss of SOCS3 gene expression converts STAT3 function from anti-apoptotic to pro-apoptotic,” The Journal of Biological Chemistry, vol. 281, no. 48, pp. 36683–36690, 2006. View at Publisher · View at Google Scholar · View at Scopus
  31. H. Qin, W.-I. Yeh, P. de Sarno et al., “Signal transducer and activator of transcription-3/suppressor of cytokine signaling-3 (STAT3/SOCS3) axis in myeloid cells regulates neuroinflammation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 13, pp. 5004–5009, 2012. View at Publisher · View at Google Scholar · View at Scopus
  32. H. Li and X. Lin, “Positive and negative signaling components involved in TNFα-induced NF-κB activation,” Cytokine, vol. 41, no. 1, pp. 1–8, 2008. View at Publisher · View at Google Scholar · View at Scopus
  33. F. M. LaFerla, “Calcium dyshomeostasis and intracellular signalling in Alzheimer's disease,” Nature Reviews Neuroscience, vol. 3, no. 11, pp. 862–872, 2002. View at Publisher · View at Google Scholar · View at Scopus
  34. V. Gerke, C. E. Creutz, and S. E. Moss, “Annexins: linking Ca2+ signalling to membrane dynamics,” Nature Reviews Molecular Cell Biology, vol. 6, no. 6, pp. 449–461, 2005. View at Publisher · View at Google Scholar · View at Scopus
  35. L. Hadri, R. G. Kratlian, L. Benard et al., “Therapeutic efficacy of AAV1.SERCA2a in monocrotaline-induced pulmonary arterial hypertension,” Circulation, vol. 128, no. 5, pp. 512–523, 2013. View at Publisher · View at Google Scholar · View at Scopus
  36. E. M. Lynes, A. Raturi, M. Shenkman et al., “Palmitoylation is the switch that assigns calnexin to quality control or ER Ca2+ signaling,” Journal of Cell Science, vol. 126, no. 17, pp. 3893–3903, 2013. View at Publisher · View at Google Scholar · View at Scopus
  37. Z.-H. Feng, J. Hao, L. Ye et al., “Overexpression of μ-calpain in the anterior temporal neocortex of patients with intractable epilepsy correlates with clinicopathological characteristics,” Seizure, vol. 20, no. 5, pp. 395–401, 2011. View at Publisher · View at Google Scholar · View at Scopus
  38. U. A. Khan, L. Liu, F. A. Provenzano et al., “Molecular drivers and cortical spread of lateral entorhinal cortex dysfunction in preclinical Alzheimer's disease,” Nature Neuroscience, vol. 17, no. 2, pp. 304–311, 2014. View at Publisher · View at Google Scholar · View at Scopus
  39. G. Daum, I. Eisenmann-Tappe, H. W. Fries, J. Troppmair, and U. R. Rapp, “The ins and outs of Raf kinases,” Trends in Biochemical Sciences, vol. 19, no. 11, pp. 474–480, 1994. View at Publisher · View at Google Scholar · View at Scopus
  40. P. Chen, K. Huang, G. Zhou et al., “Common SNPs in CSF2RB are associated with major depression and schizophrenia in the Chinese Han population,” World Journal of Biological Psychiatry, vol. 12, no. 3, pp. 233–238, 2011. View at Publisher · View at Google Scholar · View at Scopus
  41. T. F. Franke, S.-I. Yang, T. O. Chan et al., “The protein kinase encoded by the Akt proto-oncogene is a target of the PDGF-activated phosphatidylinositol 3-kinase,” Cell, vol. 81, no. 5, pp. 727–736, 1995. View at Publisher · View at Google Scholar · View at Scopus
  42. H. Dudek, S. R. Datta, T. F. Franke et al., “Regulation of neuronal survival by the serine-threonine protein kinase Akt,” Science, vol. 275, no. 5300, pp. 661–665, 1997. View at Publisher · View at Google Scholar · View at Scopus
  43. W. A. Suzuki, “The anatomy, physiology and functions of the perirhinal cortex,” Current Opinion in Neurobiology, vol. 6, no. 2, pp. 179–186, 1996. View at Publisher · View at Google Scholar · View at Scopus
  44. R. R. Hampton, “Monkey perirhinal cortex is critical for visual memory, but not for visual perception: reexamination of the behavioural evidence from monkeys,” Quarterly Journal of Experimental Psychology Section B: Comparative and Physiological Psychology, vol. 58, no. 3-4, pp. 283–299, 2005. View at Publisher · View at Google Scholar · View at Scopus
  45. A. L. Gartel and S. K. Radhakrishnan, “Lost in transcription: p21 repression, mechanisms, and consequences,” Cancer Research, vol. 65, no. 10, pp. 3980–3985, 2005. View at Publisher · View at Google Scholar · View at Scopus
  46. Y. H. Jin, K. J. Yoo, Y. H. Lee, and S. K. Lee, “Caspase 3-mediated cleavage of p21(WAF1/CIP1) associated with the cyclin A-cyclin-dependent kinase 2 complex is a prerequisite for apoptosis in SK-HEP-1 cells,” The Journal of Biological Chemistry, vol. 275, no. 39, pp. 30256–30263, 2000. View at Publisher · View at Google Scholar · View at Scopus
  47. M. Goedert, C. M. Wischik, R. A. Crowther, J. E. Walker, and A. Klug, “Cloning and sequencing of the cDNA encoding a core protein of the paired helical filament of Alzheimer disease: Identification as the microtubule-associated protein tau,” Proceedings of the National Academy of Sciences of the United States of America, vol. 85, no. 11, pp. 4051–4055, 1988. View at Publisher · View at Google Scholar · View at Scopus
  48. M. Goedert, M. G. Spillantini, R. Jakes, D. Rutherford, and R. A. Crowther, “Multiple isoforms of human microtubule-associated protein tau: sequences and localization in neurofibrillary tangles of Alzheimer's disease,” Neuron, vol. 3, no. 4, pp. 519–526, 1989. View at Publisher · View at Google Scholar · View at Scopus
  49. A. E. Vidal, S. Boiteux, I. D. Hickson, and J. P. Radicella, “XRCC1 coordinates the initial and late stages of DNA abasic site repair through protein-protein interactions,” The EMBO Journal, vol. 20, no. 22, pp. 6530–6539, 2001. View at Publisher · View at Google Scholar · View at Scopus
  50. W. H. Tang, J. Stitham, Y. Jin et al., “Aldose reductase-mediated phosphorylation of p53 leads to mitochondrial dysfunction and damage in diabetic platelets,” Circulation, vol. 129, no. 15, pp. 1598–1609, 2014. View at Publisher · View at Google Scholar · View at Scopus
  51. I. H. Ismail, R. Davidson, J. P. Gagné et al., “Germline mutations in BAP1 impair its function in DNA double-strand break repair,” Cancer Research, vol. 74, no. 16, pp. 4282–4294, 2014. View at Google Scholar
  52. A. Liede, B. Y. Karlan, and S. A. Narod, “Cancer risks for male carriers of germline mutations in BRCA1 or BRCA2: a review of the literature,” Journal of Clinical Oncology, vol. 22, no. 4, pp. 735–742, 2004. View at Publisher · View at Google Scholar · View at Scopus
  53. C. J. Sherr, H. Matsushime, and M. F. Roussel, “Regulation of CYL/cyclin D genes by colony-stimulating factor 1,” Ciba Foundation Symposium, vol. 170, pp. 209–219, 1992. View at Google Scholar · View at Scopus
  54. I. I. Goldberg, M. Harel, and R. Malach, “When the brain loses its self: prefrontal inactivation during sensorimotor processing,” Neuron, vol. 50, no. 2, pp. 329–339, 2006. View at Publisher · View at Google Scholar · View at Scopus
  55. A. Graziani, M. Poteser, W.-M. Heupel et al., “Cell-cell contact formation governs Ca2+ signaling by TRPC4 in the vascular endothelium: evidence for a regulatory TRPC4-β-catenin interaction,” The Journal of Biological Chemistry, vol. 285, no. 6, pp. 4213–4223, 2010. View at Publisher · View at Google Scholar · View at Scopus
  56. C. Redies and M. Takeichi, “Cadherins in the developing central nervous system: an adhesive code for segmental and functional subdivisions,” Developmental Biology, vol. 180, no. 2, pp. 413–423, 1996. View at Publisher · View at Google Scholar · View at Scopus
  57. R. Cao, Q. Ding, P. Li et al., “SHP1-mediated cell cycle redistribution inhibits radiosensitivity of non-small cell lung cancer,” Radiation Oncology, vol. 8, no. 1, article 178, 2013. View at Publisher · View at Google Scholar · View at Scopus
  58. L. Sooman, S. Ekman, G. Tsakonas et al., “PTPN6 expression is epigenetically regulated and influences survival and response to chemotherapy in high-grade gliomas,” Tumor Biology, vol. 35, no. 5, pp. 4479–4488, 2014. View at Publisher · View at Google Scholar · View at Scopus