A web-based integrative transcriptome analysis, RNAseqChef, uncovers the cell/tissue type-dependent action of sulforaphane
Etoh K, Nakao M
The Journal of biological chemistry · 80 citations
Review labels
Neutral facts our review recorded about how this study was done. They describe method, never whether we like the result.
How it was studied
- Design
- Meta-analysis (classified by our AI screen)
- Studied in
- Animals
- Main outcome
- Mechanisms only
Who paid for it
- Funding
- Independent funding
- Government
- Ministry of Education, Culture, Sports, Science and Technology
- University or hospital
- Kumamoto University
- Government
- Japan Society for the Promotion of Science
- Grants
- Japan Society for the Promotion of Science (20KK0185); Ministry of Education, Culture, Sports, Science and Technology (20K16145); Japan Society for the Promotion of Science (20K16145); Japan Society for the Promotion of Science (21H02686)
Based on 3 listed funder(s) and full-text disclosure statement.
Publication
- Published
- 2023-05-10 · J Biol Chem · vol. 299 · issue 6 · p. 104810
- Publisher
- Elsevier BV
- Cited
- 100 citations · more than 99% of similar papers · 9.2× the field average
- Impact
- Top 10% most cited in its field
- References
- 54 works
- Access
- Open access (journal) · CC-BY
- Research areas
- Genomics, phytochemicals, and oxidative stress · Immune Cell Function and Interaction · RNA regulation and disease
- Keywords
- Sulforaphane, Transcriptome, Action (physics), Biology, Computational biology, Chemistry, Cell biology, Genetics, Botany, Gene expression, Gene, Physics
- MeSH
- muscle, skeletal, liver, animals, mice, mice, obese, isothiocyanates, sulfoxides, antioxidants, reproducibility of results, gene expression profiling, organ specificity, internet, software, nf-e2-related factor 2, activating transcription factor 6, unfolded protein response, data visualization, rna-seq
2 authors
From JP
- Kan EtohKumamoto University
- Mitsuyoshi Nakao · correspondingKumamoto University
Abstract
RNA sequencing (RNA-seq) is a powerful technique for understanding cellular state and dynamics. However, comprehensive transcriptomic characterization of multiple RNA-seq datasets is laborious without bioinformatics training and skills. To remove the barriers to sequence data analysis in the research community, we have developed "RNAseqChef" (RNA-seq data controller highlighting expression features), a web-based platform of systematic transcriptome analysis that can automatically detect, integrate, and visualize differentially expressed genes and their biological functions. To validate its versatile performance, we examined the pharmacological action of sulforaphane (SFN), a natural isothiocyanate, on various types of cells and mouse tissues using multiple datasets in vitro and in vivo. Notably, SFN treatment upregulated the ATF6-mediated unfolded protein response in the liver and the NRF2-mediated antioxidant response in the skeletal muscle of diet-induced obese mice. In contrast, the commonly downregulated pathways included collagen synthesis and circadian rhythms in the tissues tested. On the server of RNAseqChef, we simply evaluated and visualized all analyzing data and discovered the NRF2-independent action of SFN. Collectively, RNAseqChef provides an easy-to-use open resource that identifies context-dependent transcriptomic features and standardizes data assessment.
Abstract via Europe PMC. Copyright remains with the authors or publisher (CC BY).
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