Although genomic technologies have advanced the characterization of
gene regulatory networks downstream of transcription factors, the
identification of pathways upstream of these transcription factors has
been more challenging. In this study we present a gene signature-based
approach for connecting signaling pathways to transcription factors,
as exemplified by p73. We generated a p73 gene signature by
integrating whole-genome chromatin immunoprecipitation and expression
profiling. The p73 signature was linked to corresponding signatures
produced by drug candidates, using the in silico Connectivity Map
resource, to identify drugs that would induce p73 activity. Of the
pharmaceutical agents identified, there was enrichment for direct or
indirect inhibitors of mammalian Target of Rapamycin (mTOR) signaling.
Treatment of both primary cells and cancer cell lines with rapamycin,
metformin, and pyrvinium resulted in an increase in p73 levels, as did
RNA interference-mediated knockdown of mTOR. Further, a subset of
genes associated with insulin response or autophagy exhibited mTOR-
mediated, p73-dependent expression. Thus, downstream gene signatures
can be used to identify upstream regulators of transcription factor
activity, and in doing so, we identified a new link between mTOR, p73,
and p73-regulated genes associated with autophagy and metabolic
pathways.