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Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis
journal contribution
posted on 2019-12-13, 16:49 authored by Michael Burkard, Alexander Betz, Kristin Schirmer, Anze ZupanicThe use of omics is gaining importance in the field of
nanoecotoxicology;
an increasing number of studies are aiming to investigate the effects
and modes of action of engineered nanomaterials (ENMs) in this way.
However, a systematic synthesis of the outcome of such studies regarding
common responses and toxicity pathways is currently lacking. We developed
an R-scripted computational pipeline to perform reanalysis and functional
analysis of relevant transcriptomic data sets using a common approach,
independent from the ENM type, and across different organisms, including Arabidopsis thaliana, Caenorhabditis
elegans, and Danio rerio. Using the pipeline that can semiautomatically process data from
different microarray technologies, we were able to determine the most
common molecular mechanisms of nanotoxicity across extremely variable
data sets. As expected, we found known mechanisms, such as interference
with energy generation, oxidative stress, disruption of DNA synthesis,
and activation of DNA-repair but also discovered that some less-described
molecular responses to ENMs, such as DNA/RNA methylation, protein
folding, and interference with neurological functions, are present
across the different studies. Results were visualized in radar charts
to assess toxicological response patterns allowing the comparison
of different organisms and ENM types. This can be helpful to retrieve
ENM-related hazard information and thus fill knowledge gaps in a comprehensive
way in regard to the molecular underpinnings and mechanistic understanding
of nanotoxicity.
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data setsnanotoxicityENM typesknowledge gapsmicroarray technologiesCaenorhabditis elegansEngineered NanomaterialsCommon Gene Expression Patternstoxicological response patternsArabidopsis thalianaDanio reriointerferencetoxicity pathwaysENM-related hazard informationpipelineradar chartsENM typesemiautomatically process dataoxidative stresstranscriptomic data setsDNA synthesisEnvironmental Model Organisms Exposedmechanismenergy generationorganism
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