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

Hidenori Tani, Taro Matsutani, Hiroshi Aoki, Kaoru Nakamura, Yu Hamaguchi, Tetsuya Nakazato, Michiaki Hamada

Research output: Contribution to journalArticle

Abstract

For chemical safety screening, there is a need for more efficient assays that do not involve animals. Among the alternatives to animal testing, in vitro cell-based assays are among the most appropriate to screen the toxicity of chemicals. Previous studies focused on mRNAs as biomarkers; however, recent whole-transcriptome analyses have revealed the presence of a large number of unannotated noncoding RNAs (ncRNAs) that appear not to have any protein-coding potential. Here, we used deep sequencing analysis (RNA-seq) to identify novel RNA biomarkers, including ncRNAs, that exhibited a substantial response to chemical toxicity from nine chemicals [benzene, bis(2-ethylhexyl)phthalate, chloroform, p-cresol, p-dichlorobenzene, phenol, pyrocatechol, tri-n-butyl phosphate, and trichloroethylene]. We used neural cells derived from mouse embryonic stem cells (mESCs) as a cell-based assay for chemical safety screening. RNA-seq revealed that some ncRNAs responded substantially to the chemical compounds in neural cells derived from mESCs. This indicates that the ncRNAs can be used as novel RNA biomarkers for chemical safety screening.

Original languageEnglish
JournalBiochemical and Biophysical Research Communications
DOIs
Publication statusAccepted/In press - 2018 Jan 1

Fingerprint

Chemical Safety
RNA Sequence Analysis
High-Throughput Nucleotide Sequencing
Untranslated RNA
Biomarkers
Stem cells
Screening
RNA
Assays
Animal Testing Alternatives
Diethylhexyl Phthalate
Toxicity
Animals
Trichloroethylene
Gene Expression Profiling
Chloroform
Phenol
Benzene
Chemical compounds
Messenger RNA

Keywords

  • Cell-based assay
  • Chemical safety
  • Noncoding RNA
  • RNA-Seq

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

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AU - Aoki, Hiroshi

AU - Nakamura, Kaoru

AU - Hamaguchi, Yu

AU - Nakazato, Tetsuya

AU - Hamada, Michiaki

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