The autophagic process, which can facilitate breast cancer resistance to endocrine, cytotoxic,
and molecularly targeted agents, is mainly regulated at the post-translational level. Although
recent studies have suggested a possible transcriptome regulation of the autophagic genes, little is
known about either the analysis tools that can be applied or the functional importance of putative
candidate genes emerging from autophagy-dedicated transcriptome studies. In this context, we
evaluated whether the constitutive activation of the autophagy machinery, as revealed by a
transcriptome analysis using an autophagy-focused polymerase chain reaction (PCR) array, might allow
for the identification of novel autophagy-specific biomarkers for intrinsic (primary) resistance to
HER2-targeted therapies. Quantitative real-time PCR (qRT-PCR)-based profiling of 84 genes involved
in autophagy revealed that, when compared to trastuzumab-sensitive SKBR3 cells, the positive
regulator of autophagic vesicle formation ATG12 (autophagy-related gene 12) was the
most differentially up-regulated gene in JIMT1 cells, a model of intrinsic cross-resistance to
trastuzumab and other HER1/2-targeting drugs. An analysis of the transcriptional status of
ATG12 in > 50 breast cancer cell lines suggested that the
ATG12 transcript is commonly upregulated in trastuzumab-unresponsive
HER2-overexpressing breast cancer cells. A lentiviral-delivered small hairpin RNA stable knockdown
of the ATG12 gene fully suppressed the refractoriness of JIMT1 cells to
trastuzumab, erlotinib, gefitinib, and lapatinib in vitro. ATG12 silencing
significantly reduced JIMT1 tumor growth induced by subcutaneous injection in nude mice. Remarkably,
the outgrowth of trastuzumab-unresponsive tumors was prevented completely when trastuzumab treatment
was administered in an ATG12-silenced genetic background. We demonstrate for the
first time the usefulness of low-density, autophagy-dedicated qRT-PCR-based platforms for monitoring
primary resistance to HER2-targeted therapies by transcriptionally screening the autophagy
interactome. The degree of predictive accuracy warrants further investigation in the clinical
situation.