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Genome-wide transcriptional comparison of MPP+ treated human neuroblastoma cells with the state space model

Department of Biomolecular and Chemical Engineering, DongYang University, Yeongju 750-711, South Korea

Special Issues: Cell Signalling and Neuronal Cell Death

This study compared a parkinsonian neurotoxin 1-methyl-4-phenylpyridinium (MPP+) response in two distinct phenotypes of human neuroblastoma cell lines: neuronal N-type SH-SY5Y cells and flat substrate-adherent S-type SH-EP cells. SH-SY5Y and SH-EP cells shared only 14% of their own MPP+ response genes, and their gene ontology (GO) analysis revealed significant endoplasmic reticulum (ER) stress by misfolded proteins. Gene modules, which are groups of transcriptionally co-expressed genes with similar biological functions, were identified for SH-SY5Y and SH-EP cells by using time-series microarray data with the state space model (SSM). All modules of SH-SY5Y and SH-EP cells showed strong positive auto-regulation that was often mediated via signal molecules and may cause bi-stability. Interactions in gene levels were calculated by using SSM parameters obtained in the process of module identification. Gene networks that were constructed from the gene interaction matrix showed different hub genes with high node degrees between SH-SY5Y and SH-EP cells. That is, key hub genes of SH-SY5Y cells were DCN, HIST1H2BK, and C5orf40, whereas those of SH-EP cells were MSH6, RBCK1, MTHFD2, ZNF26, CTH, and CARS. These results suggest that inhibition of the mitochondrial complex I by MPP+ might induce different downstream processes that are cell type dependent.
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References

1. Dawson TM, Ko HS, Dawson VL (2010) Genetic animal models of Parkinson's disease. Neuron 66: 646-661.    

2. Ribeiro RP, Moreira EL, Santos DB, et al. (2003) Probucol affords neuroprotection in a 6-OHDA mouse model of Parkinson's disease. Neurochem Res 38: 660-668.    

3. Lu C, Zhang J, Shi X, et al. (2014) Neuroprotective effects of tetramethylpyrazine against dopaminergic neuron injury in a rat model of Parkinson's disease induced by MPTP. Int J Biol Sci 10: 350-357.    

4. Langston JW, Ballard P, Tetrud JW, et al. (1983) Parkinsonism in humans due to a product of meperidine- analog synthesis. Science 219: 979-980.    

5. Dagda RK, Das Banerjee T, Janda E (2013) How Parkinsonian toxins dysregulate the autophagy machinery. Int J Mol Sci 14: 22163-22189.    

6. Behl C, Davies JB, Lesley R, et al. (1994) Hydrogen peroxide mediates amyloid protein toxicity. Cell 77: 817-827.    

7. Xiang W, Schlachetzki JC, Helling S, et al. (2013) Oxidative stress-induced posttranslational modifications of alpha-synuclein: Specific modification of alpha-synuclein by 4-hydroxy-2-nonenal increases dopaminergic toxicity. Mol Cell Neurosci 54: 71-83.    

8. Zhou M, Xu S, Mi J, et al. (2013) Nuclear translocation of alpha-synuclein increases susceptibility of MES23.5 cells to oxidative stress. Brain Res 1500: 19-27.    

9. Varcin M, Bentea E, Michotte Y, et al. (2012) Oxidative stress in genetic mouse models of Parkinson's disease. Oxid Med Cell Longev 2012: 624925-.    

10. Perier C, Bové J, Vila M (2012) Mitochondria and programmed cell death in Parkinson's disease: apoptosis and beyond. Antioxid Redox Signal 16: 883-895.    

11. Chakraborty S, Bornhorst J, Nguyen TT, et al. (2013) Oxidative stress mechanisms underlying Parkinson's disease-associated neurodegeneration in C. elegans. Int J Mol Sci 14: 23103-23128.    

12. Kim IS, Choi D.-K., Do J.H. (2013) Genome-wide temporal responses of human neuroblastoma SH-SY5Y cells MPP+ neurotoxicity. BioChip J 7: 247-257.    

13. Do JH (2014) Neurotoxin-induced pathway perturbation in human neuroblastoma SH-EP cells. Mol Cells 37: 672-684.    

14. Do JH, Kim IS, Lee JD, et al. (2011) Comparison of genomic profiles in human neuroblastic SH-SY5Y and substrate-adherent SH-EP cells using array comparative genomic hybridization. BioChip J 5: 165-174.    

15. Hirose O, Yoshida R, Imoto S, et al. (2008) Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics 24: 932-942.    

16. Leek JT, Monsen E, Dabney AR, et al. (2006) EDGE: extraction and analysis of differential gene expression. Bioinformatics 22: 507-508.    

17. Eden E, Navon R, Steinfeld I, et al. (2009) Gorilla: a tool for discovery and visualization of enriched GO terms in ranked gene list. BMC Bioinformatics 10: 48.    

18. Yamaguchi R, Yoshida R, Imoto S, et al. (2007) Finding module-based gene networks with state-space models. IEEE Signal Proc Mag 24: 37-46.    

19. Tamada Y, Yamaguchi R, Imoto S, et al. (2011) SiGN-SSM: open source parallel software for estimating gene networks with state space model. Bioinformatics 27: 1172-1173.    

20. Kovács IA, Palotai R, Szalay MS, et al. (2010) Community landscapes: an integrative approach to determine overlapping network module hierarchy, identify key nodes and predict network dynamics. PLoS One 5: e12528.    

21. Wang X, Dalkic E, Wu M, et al. (2008) Gene-module analysis: identification to networks and dynamics. Curr Opin Biotechnol 19: 482-491.    

22. Pinho R, Garcia V, Irimia M, et al. (2014) Stability depends on positive autoregulation in Boolean gene regulatory networks. PLoS Comput Biol 10: e1003916.    

23. Iaccarino I, Marra G, Palombo F, et al (1998) hMSH2 and hMSH6 play distinct roles in mismatch binding and contribute differently to the ATPase activity of hMutSalpha. EMBO J 17: 2677-2686.    

24. Ardley HC, Robinson PA (2005) E3 ubiquitin ligases. Essays Biochem. 41: 15-30.    

25. Wu DC, Jackson-Lewis V, Vila M, et al. (2002) Blockage of microglial activation is neuroprotective in the 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine mouse model of Parkinson disease. J Neurosci 22: 1763-1771.

26. Perier C, Tieu K, Guégan C, et al. (2005) Complex I deficiency primes Bax-dependent neuronal apoptosis through mitochondrial oxidative damage. Proc Natl Acad Sci USA 102: 19126-19131.    

27. Hoang T, Choi DK, Nagai M, et al. (2009) Neuronal NOS and cyclooxygenase-2 contribute to DNA damage in a mouse model of Parkinson disease. Free Radic Biol Med 47: 1049-1056.    

28. Shinohara T, Nagashima K, Major EO (1997) Propagation of the human polyomavirus, JCV, in human neuroblastoma cell lines. Virology 228: 269-277.    

29. Hondele M, Ladurner AG (2011) The chaperone-histone partnership: for the greater good of histone traffic and chromatin plasticity. Curr Opin Struct Biol 21: 698–708.    

30. Smith KT, Workman JL (2012) Chromatin proteins: key responders to stress. PLoS Biol 10: e1001371.    

Copyright Info: © 2015, Jin Hwan Do, licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution Licese (http://creativecommons.org/licenses/by/4.0)

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