Genome-wide transcriptional comparison of MPP<sup>+</sup> treated human neuroblastoma cells with the state space model
This study compared a parkinsonian neurotoxin 1-methyl-4-phenylpyridinium (MPP<sup>+</sup>) 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 thei...
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| Format: | Article |
| Language: | English |
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AIMS Press
2015-10-01
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| Series: | AIMS Molecular Science |
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| Online Access: | http://www.aimspress.com/Molecular/article/483/fulltext.html |
| _version_ | 1818491913680977920 |
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| author | Jin Hwan Do |
| author_facet | Jin Hwan Do |
| author_sort | Jin Hwan Do |
| collection | DOAJ |
| description | This study compared a parkinsonian neurotoxin 1-methyl-4-phenylpyridinium (MPP<sup>+</sup>) 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<sup>+</sup> 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<i> DCN</i>, <i>HIST1H2BK</i>, and <i>C5orf40</i>, whereas those of SH-EP cells were<i> MSH6</i>, <i>RBCK1</i>, <i>MTHFD2</i>, <i>ZNF26</i>, <i>CTH</i>, and <i>CARS</i>. These results suggest that inhibition of the mitochondrial complex I by MPP<sup>+</sup> might induce different downstream processes that are cell type dependent. |
| first_indexed | 2024-12-10T17:36:48Z |
| format | Article |
| id | doaj.art-b704487817674d92b22efdb7f0ab60a3 |
| institution | Directory Open Access Journal |
| issn | 2372-0301 |
| language | English |
| last_indexed | 2024-12-10T17:36:48Z |
| publishDate | 2015-10-01 |
| publisher | AIMS Press |
| record_format | Article |
| series | AIMS Molecular Science |
| spelling | doaj.art-b704487817674d92b22efdb7f0ab60a32022-12-22T01:39:31ZengAIMS PressAIMS Molecular Science2372-03012015-10-012444046010.3934/molsci.2015.4.440201504440Genome-wide transcriptional comparison of MPP<sup>+</sup> treated human neuroblastoma cells with the state space modelJin Hwan Do0Department of Biomolecular and Chemical Engineering, DongYang University, Yeongju 750-711, South KoreaThis study compared a parkinsonian neurotoxin 1-methyl-4-phenylpyridinium (MPP<sup>+</sup>) 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<sup>+</sup> 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<i> DCN</i>, <i>HIST1H2BK</i>, and <i>C5orf40</i>, whereas those of SH-EP cells were<i> MSH6</i>, <i>RBCK1</i>, <i>MTHFD2</i>, <i>ZNF26</i>, <i>CTH</i>, and <i>CARS</i>. These results suggest that inhibition of the mitochondrial complex I by MPP<sup>+</sup> might induce different downstream processes that are cell type dependent.http://www.aimspress.com/Molecular/article/483/fulltext.htmlneuroblastoma1-methyl-4-phenylpyridiniumcell deathParkinson's diseasetranscriptional regulationgene networksstate space model |
| spellingShingle | Jin Hwan Do Genome-wide transcriptional comparison of MPP<sup>+</sup> treated human neuroblastoma cells with the state space model AIMS Molecular Science neuroblastoma 1-methyl-4-phenylpyridinium cell death Parkinson's disease transcriptional regulation gene networks state space model |
| title | Genome-wide transcriptional comparison of MPP<sup>+</sup> treated human neuroblastoma cells with the state space model |
| title_full | Genome-wide transcriptional comparison of MPP<sup>+</sup> treated human neuroblastoma cells with the state space model |
| title_fullStr | Genome-wide transcriptional comparison of MPP<sup>+</sup> treated human neuroblastoma cells with the state space model |
| title_full_unstemmed | Genome-wide transcriptional comparison of MPP<sup>+</sup> treated human neuroblastoma cells with the state space model |
| title_short | Genome-wide transcriptional comparison of MPP<sup>+</sup> treated human neuroblastoma cells with the state space model |
| title_sort | genome wide transcriptional comparison of mpp sup sup treated human neuroblastoma cells with the state space model |
| topic | neuroblastoma 1-methyl-4-phenylpyridinium cell death Parkinson's disease transcriptional regulation gene networks state space model |
| url | http://www.aimspress.com/Molecular/article/483/fulltext.html |
| work_keys_str_mv | AT jinhwando genomewidetranscriptionalcomparisonofmppsupsuptreatedhumanneuroblastomacellswiththestatespacemodel |