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Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-fixed paraffin-embedded (FFPE) Samples
Citation:
Bhat, V., S. Hester, B. Chorley, G. Carswell, W. Jones, AND C. Wood. Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-fixed paraffin-embedded (FFPE) Samples. FutureToxIII, Arlington, VA, November 19 - 20, 2015.
Impact/Purpose:
This represents a novel way of deriving Bench-mark dose estimates from genomic data. By doing so, it provides quantitative dose estimates for marker gene and pathway activation.
Description:
Formalin-fixed paraffin-embedded (FFPE) samples provide a vast untapped resource for chemical safety and translational science. To date, genomic profiling of FFPE samples has been limited by poor RNA quality and inconsistent results with limited utility in dose-response assessment. Here we used RNA-Seq to evaluate transcriptomic dose-response profiles from paired FFPE and frozen (FROZ) liver samples (n=16 each) from mice treated for 7 d with control diet or with 3 dose levels of di(2-ethylhexyl)phthalate, a well-studied PPARalpha activator. Previous research found these FFPE and FROZ samples to have comparable sequencing quality metrics, fold changes for genes, and enrichment of signaling pathways: PPARalpha & cholesterol-related predominated. In the present study, benchmark dose-response (BMD) analysis of marker genes (Acot and Cyp4a series) and associated pathways showed strong concordance of potency estimates between FFPE and FROZ and with potency estimates for downstream mode of action key events from longer-term studies. For example, BMD estimates for Cyp4a marker genes at 7 d were ~43-63 mg/kg-d for FROZ and 57-76 mg/kg-d for FFPE compared to the BMD of 71 mg/kg-d for hepatocellular carcinomas at two years. Median pathway BMD estimates for PPARalpha signaling at 7 d were 156 mg/kg-d for FROZ and 102 mg/kg-d for FFPE. Median pathway BMD estimates for fatty acid B-oxidation were 74 mg/kg-d for FROZ and 94 mg/kg-d for FFPE. These findings should help broaden the utility of archival resources in toxicological science. This abstract does not reflect EPA policy.