RNA-Seq Can Be Used to Quantify Gene Expression Levels for Use in the GARDskin Assay.

Area of Science:

• Toxicology
• Genomics
• In vitro assays

Background:

• Non-animal methods for skin sensitizer identification are advancing.
• The GARDskin assay currently uses targeted gene expression for hazard classification.
• Next-generation sequencing offers new possibilities for gene expression analysis.

Purpose of the Study:

• To evaluate RNA sequencing (RNA-seq) as a gene expression quantification method for the GARDskin assay.
• To compare RNA-seq data with the current NanoString nCounter platform.
• To assess the reliability of RNA-seq for skin sensitizer hazard classification.

Main Methods:

• RNA-seq was performed on 24 paired samples previously analyzed by NanoString nCounter.
• Gene expression profiles from both platforms were compared.
• RNA-seq data was used with the standard GARDskin analysis pipeline for hazard classification.

Main Results:

• Gene expression profiles from RNA-seq and NanoString were highly similar (Spearman's rho=0.95, Lin's CCC=0.87).
• RNA-seq data successfully classified the sensitizing hazard of 24 treatments.
• Classifications using RNA-seq data completely corresponded with reference classifications.

Conclusions:

• RNA-seq data strongly resembles NanoString nCounter data.
• RNA-seq can be reliably used for hazard classifications within the GARDskin assay.
• This validates RNA-seq as a viable alternative for gene expression quantification in non-animal testing.