POL and Z1031 Gene Expression_Final

Background: Unlike estrogen receptor (ER) negative breast cancer, ER-positive breast cancer outcomes are less influenced by lymphocyte content, indicating a need for investigation of checkpoint targets and immune tolerance mechanisms that may be specific to this disease subset. Methods: A supervised analysis of microarray data from the Alliance/ACOSOG Z1031 trial was conducted to identify upregulated genes in Luminal B breast cancers that exhibited persistent tumor proliferation despite aromatase inhibitor therapy (33 cases Ki67 >10%) versus Luminal B breast cancers that were more sensitive (33 cases Ki67 <10%). Results: This study identified thirty genes (Pearson’s r>0.4 with Ki67 as a continuous variable). These genes were enriched for immune tolerance processes (p<0.005) and three targetable immune checkpoint components were upregulated in resistant cases: IDO1, LAG3, and PD1. High IDO1 mRNA associated with poor prognosis in ER+ disease across two independent cohorts (METABRIC and TCGA). Furthermore, analysis indicated IDO1 was tightly associated with IFN-γ/STAT1 signaling.  As a composite immune tolerance signature, expression of these pathway components associated with higher baseline Ki67 and lower ER, PgR levels and poor disease specific survival.  In tissue microarray analysis, IDO1 was observed in stromal cells and tumor-associated macrophages, with a higher incidence in Luminal B cases.  Further mRNA and tissue microarray analyses associated IDO1 expression with the presence of macrophages (M1 by CIBERSORT) and regulatory T cells. Conclusion: Targetable immune-checkpoint components are upregulated in majority of neoadjuvant endocrine therapy resistant Luminal B cases. Our findings suggests potential for immune checkpoint inhibitors in poor outcome ER+ breast cancer. 603 microarray experiments from 468 breast cancer patients were profiled using 2 channel (tumor:reference) whole human genome Agilent arrays. Timepoints include baseline (BL), 2-4 weeks post endocrine treatment (w2, M, or 4wk), and surgery (S = ~16 weeks post endocrine therapy).