Identification of RNA biomarkers for chemical safety screening in mouse embryonic stem cells using RNA deep sequencing analysis

• Published in: PloS one 2017-07, Vol.12 (7), p.e0182032
• Main Authors: Tani, Hidenori, Takeshita, Jun-Ichi, Aoki, Hiroshi, Nakamura, Kaoru, Abe, Ryosuke, Toyoda, Akinobu, Endo, Yasunori, Miyamoto, Sadaaki, Gamo, Masashi, Sato, Hiroaki, Torimura, Masaki
• Format: Article
• Language: English
• Subjects: Animal research; Animals; Benzene; Benzene - toxicity; Biocompatibility; Bioindicators; Biological markers; Biology and Life Sciences; Biomarkers; Biomarkers - metabolism; Cell division; Cell Line; Chemical compounds; Chemical Safety; Chemicals; Down-Regulation - drug effects; Down-Regulation - genetics; Embryo cells; Embryonic stem cells; Engineering schools; Environmental management; Gene expression; Gene Ontology; Gene sequencing; Genomics; High-Throughput Nucleotide Sequencing - methods; Hydrocarbons; In vivo methods and tests; Leukemia; Medical screening; Messenger RNA; Mice; Mice, Inbred C57BL; MicroRNAs; Mouse Embryonic Stem Cells - drug effects; Mouse Embryonic Stem Cells - metabolism; Phenols; Physical Sciences; Physiological aspects; Pollutants; Properties; Pulmonary arteries; Ribonucleic acid; RNA; RNA - genetics; RNA - metabolism; RNA polymerase; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Untranslated - genetics; RNA, Untranslated - metabolism; Safety; Stem cell transplantation; Stem cells; Toxicity; Toxicity testing; Up-Regulation - drug effects; Up-Regulation - genetics
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0182032

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.