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E-GEOD-63552 - Extensive temporal transcriptome and microRNA analyses identify molecular mechanisms underlying mitochondrial dysfunction induced by multi-walled carbon nanotubes in human lung cells (Affymetrix)

Status
Released on 2 April 2015, last updated on 3 April 2015
Organism
Homo sapiens
Samples (123)
Array (1)
Protocols (6)
Description
Understanding toxicity pathways of engineered nanomaterials (ENM) has recently been brought forward as a key step in 21st century ENM risk assessment. Molecular mechanisms linked to phenotypic end points is a step towards the development of toxicity tests based on key events, which may allow for grouping of ENM according to their mechanisms of action. This study identified molecular mechanisms underlying mitochondrial dysfunction in human bronchial epithelial BEAS 2B cells following exposure to one of the most studied multi-walled carbon nanotubes (MWCNTs; Mitsui-7). Asbestos was used as a positive control and a non-carcinogenic glass wool material was included as a negative fibre control. Decreased mitochondrial membrane potential (MMP↓) was observed for MWCNTs at a biologically relevant dose (0.25 μg/cm2) and for asbestos at 2 μg/cm2, but not for glass wool. Extensive temporal transcriptomic and microRNA expression analyses identified a 330-gene signature related to MWCNT- and asbestos-induced MMP↓. Fourty-nine of the MMP↓-associated genes showed highly similar expression patterns over time (six time points) and the majority was found to be regulated by two transcription factors strongly involved in mitochondrial homeostasis, APP and NRF1. In addition, four miRNAs were associated with MMP↓ and one of them, miR-1275, was found to negatively correlate with a large part of the MMP↓-associated genes. Cellular processes such as gluconeogenesis, glucose metabolism, mitochondrial LC-fatty acid β-oxidation and spindle microtubule function were enriched among the MMP↓-associated genes and miRNAs. These results are expected to be useful in the identification of key events in ENM-related toxicity pathways for the development of molecular screening techniques. BEAS 2B cells were exposed to 0.25 and 2 μg/cm2 of MWCNT, asbestos and glass wool (MMVF10) for 1, 4, 6, 12, 24 and 48 hours. Three independent experiments were performed to obtain a total of 3 replicates for each experimental condition. Non-exposed cells for each time point were used as controls. Three samples failed to give adequate quality RNA and a total of 123 samples were hybridized to Affymetrix GeneChip U133 Plus 24-array plates.
Experiment type
transcription profiling by array 
Contacts
Citation
Extensive temporal transcriptome and microRNA analyses identify molecular mechanisms underlying mitochondrial dysfunction induced by multi-walled carbon nanotubes in human lung cells. Nymark P, Wijshoff P, Cavill R, van Herwijnen M, Coonen ML, Claessen S, Catal�n J, Norppa H, Kleinjans JC, Bried� JJ.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-63552.idf.txt
Sample and data relationshipE-GEOD-63552.sdrf.txt
Raw data (2)E-GEOD-63552.raw.1.zip, E-GEOD-63552.raw.2.zip
Processed data (1)E-GEOD-63552.processed.1.zip
Array designA-GEOD-15798.adf.txt
Links