34 research outputs found
Identification of RNA biomarkers for chemical safety screening in mouse embryonic stem cells using RNA deep sequencing analysis
Although it is not yet possible to replace in vivo animal testing completely, the need for a more efficient method for toxicity testing, such as an in vitro cell-based assay, has been widely acknowledged. Previous studies have focused on mRNAs as biomarkers; however, recent studies have revealed that non-coding RNAs (ncRNAs) are also efficient novel biomarkers for toxicity testing. Here, we used deep sequencing analysis (RNA-seq) to identify novel RNA biomarkers, including ncRNAs, that exhibited a substantial response to general chemical toxicity from nine chemicals, and to benzene toxicity specifically. The nine chemicals are listed in the Japan Pollutant Release and Transfer Register as class I designated chemical substances. We used undifferentiated mouse embryonic stem cells (mESCs) as a simplified cell-based toxicity assay. RNA-seq revealed that many mRNAs and ncRNAs responded substantially to the chemical compounds in mESCs. This finding indicates that ncRNAs can be used as novel RNA biomarkers for chemical safety screening
Classification of chemical compounds based on the correlation between \textit{in vitro} gene expression profiles
Toxicity evaluation of chemical compounds has traditionally relied on animal
experiments;however, the demand for non-animal-based prediction methods for
toxicology of compounds is increasing worldwide. Our aim was to provide a
classification method for compounds based on \textit{in vitro} gene expression
profiles. The \textit{in vitro} gene expression data analyzed in the present
study was obtained from our previous study. The data concerned nine compounds
typically employed in chemical management.We used agglomerative hierarchical
clustering to classify the compounds;however, there was a statistical
difficulty to be overcome.We needed to properly extract RNAs for clustering
from more than 30,000 RNAs. In order to overcome this difficulty, we introduced
a combinatorial optimization problem with respect to both gene expression
levels and the correlation between gene expression profiles. Then, the
simulated annealing algorithm was used to obtain a good solution for the
problem. As a result, the nine compounds were divided into two groups using
1,000 extracted RNAs. Our proposed methodology enables read-across, one of the
frameworks for predicting toxicology, based on \textit{in vitro} gene
expression profiles.Comment: 13pages, 7 figure
Relationship between mechanical response and microscopic crack propagation behavior of hydrogen-related intergranular fracture in as-quenched martensitic steel
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