A Gene Expression Biomarker Predicts Heat Shock Factor 1 Activation in a Gene Expression Compendium

The
United States Environmental Protection Agency (US EPA) recently
developed a tiered testing strategy to use advances in high-throughput
transcriptomics (HTTr) testing to identify molecular targets of thousands
of environmental chemicals that can be linked to adverse outcomes.
Here, we describe a method that uses a gene expression biomarker to
predict chemical activation of heat shock factor 1 (HSF1), a transcription
factor critical for proteome maintenance. The HSF1 biomarker was built
from transcript profiles derived from A375 cells exposed to a HSF1-activating
heat shock protein (HSP) 90 inhibitor in the presence or absence of
HSF1 expression. The resultant 44 identified genes included those
that (1) are dependent on HSF1 for regulation, (2) have direct interactions
with HSF1 assessed by ChIP-Seq, and (3) are in the molecular chaperone
family. To test for accuracy, the biomarker was compared in a pairwise
manner to gene lists derived from treatments with known HSF1 activity
(HSP and proteasomal inhibitors) using the correlation-based Running
Fisher test; the balanced accuracy for prediction was 96%. A microarray
compendium consisting of 12,092 microarray comparisons from human
cells exposed to 2670 individual chemicals was screened using our
approach; 112 and 19 chemicals were identified as putative HSF1 activators
or suppressors, respectively, and most appear to be novel modulators.
A large percentage of the chemical treatments that induced HSF1 also
induced oxidant-activated NRF2 (∼46%). For five compounds or
mixtures, we found that NRF2 activation occurred at lower concentrations
or at earlier times than HSF1 activation, supporting the concept of
a tiered cellular protection system dependent on the level of chemical-induced
stress. The approach described here could be used to identify environmentally
relevant chemical HSF1 activators in HTTr data sets.