title: Editor's Highlight: Application of Gene Set Enrichment Analysis for Identification of Chemically Induced, Biologically Relevant Transcriptomic Networks and Potential Utilization in Human Health Risk Assessment.
abstract: The rate of new chemical development in commerce combined with a paucity of toxicity data for legacy chemicals presents a unique challenge for human health risk assessment. There is a clear need to develop new technologies and incorporate novel data streams to more efficiently inform derivation of toxicity values. One avenue of exploitation lies in the field of transcriptomics and the application of gene expression analysis to characterize biological responses to chemical exposures. In this context, gene set enrichment analysis (GSEA) was employed to evaluate tissue-specific, dose-response gene expression data generated following exposure to multiple chemicals for various durations. Patterns of transcriptional enrichment were evident across time and with increasing dose, and coordinated enrichment plausibly linked to the etiology of the biological responses was observed. GSEA was able to capture both transient and sustained transcriptional enrichment events facilitating differentiation between adaptive versus longer term molecular responses. When combined with benchmark dose (BMD) modeling of gene expression data from key drivers of biological enrichment, GSEA facilitated characterization of dose ranges required for enrichment of biologically relevant molecular signaling pathways, and promoted comparison of the activation dose ranges required for individual pathways. Median transcriptional BMD values were calculated for the most sensitive enriched pathway as well as the overall median BMD value for key gene members of significantly enriched pathways, and both were observed to be good estimates of the most sensitive apical endpoint BMD value. Together, these efforts support the application of GSEA to qualitative and quantitative human health risk assessment.
authors.affiliation: National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA.
authors.forename: Jeffry L
authors.initials: JL
authors.lastname: Dean
authors.affiliation: National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA.
authors.forename: Q Jay
authors.initials: QJ
authors.lastname: Zhao
authors.affiliation: National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA.
authors.forename: Jason C
authors.initials: JC
authors.lastname: Lambert
authors.affiliation: National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA.
authors.forename: Belinda S
authors.initials: BS
authors.lastname: Hawkins
authors.affiliation: National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA.
authors.forename: Russell S
authors.initials: RS
authors.lastname: Thomas
authors.affiliation: National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA.
authors.forename: Scott C
authors.initials: SC
authors.lastname: Wesselkamper
mesh_terms: D000818:Animals; D004305:Dose-Response Relationship, Drug; D005260:Female; D053263:Gene Regulatory Networks; D006801:Humans; D008297:Male; D051381:Rats; D011916:Rats, Inbred F344; D017207:Rats, Sprague-Dawley; D018570:Risk Assessment; D059467:Transcriptome / Q000187:drug effects*
keywords: enrichment; gene expression; human health risk assessment; toxicogenomics; transcriptomics; GSEA