Unique disease features that distinguish ER-negative breast cancer patients by AR status for successful therapeutic targeting remains poorly understood as a result of limitations and inconsistencies with protein-based AR assessment approaches. Using CBCS expression data, we designed and validated a multigene classifier that distinguishes AR-low versus AR-high ER-negative breast cancers. AR-low status in ER-negative breast cancer was significantly associated with younger age at diagnosis, Black race, HER2-negativity, high-grade, and higher ROR; these associations remained significant after adjusting for TNBC status. These findings suggest that in ER-negative breast cancers, low AR expression is associated with aggressive disease. AR-low/ER-negative tumors occur more frequently in Black (versus white) women; consequently AR-low/ER-negative breast cancer may be important for understanding racial disparities in survival. Considering other biological phenotypes, AR-low cancers in the CBCS cohort exhibited adaptive immunity enrichment and both CBCS and TCGA data sets displayed significantly greater homologous recombination repair deficiency among AR-low cancers.
Our findings are consistent with what has been previously reported for demographic factors. Park et al. reported that women, under the age of 35 years, were diagnosed with AR-negative/ER-negative breast cancer more frequently than women over the age of 35 (11.7% and 7.0%, respectively)[31]. Several groups have reported that in TNBC, AR-negativity is significantly associated with younger age at diagnosis and that older age at diagnosis is more prevalent in the luminal androgen receptor subtype and among AR-positive TNBC patients[15, 18, 19, 32–34]. Prior evidence also showed that low AR expression in ER-negative cancer is associated with Black race and West African genetic ancestry[35–37].
The prognostic role of low AR expression in TNBC remains controversial. Our findings provide evidence that AR-negative TNBC is associated with aggressive disease features such as advanced stage and high histological grade[3, 8, 10, 11]. The multi-parametric gene expression-based signature ROR-PT is derived from the PAM50 intrinsic subtype signature and has been reported to predict distant recurrence in node-negative and node-positive ER-positive breast cancer patients[38–42]. Our ROR-PT analysis aligns with previous studies showing higher incidence of recurrence or relapse in women with AR-low versus AR-high ER-negative breast cancer[8, 12, 43–46]. Yang et al. reported that AR-positivity is associated with longer relapse-free survival among HER2-negative patients[47]. Wang and colleagues showed that women with AR-low TNBC exhibited a greater incidence of distant metastases than women with AR-high TNBC[48]. Hence, our RNA-based classifier produces similar results to in studies that use IHC to define AR expression.
Another distinction observed herein between AR-negative and AR-positive TNBC was with respect to immune profiles. Consistent with our findings, Davis and colleagues previously reported that AR-negative tumors are upregulated in T cell marker (CD4 and CD8), immune checkpoint (PD1, PD-L1, and CTLA-4), and immune cell signaling pathway marker (ILR2, CCR5, NFKBII2) RNA expression compared to AR-positive tumors in TNBC[49]. These findings suggest that AR-negative TNBC may display increased numbers of infiltrating lymphocytes, but exhibit greater immunosuppression compared to AR-positive TNBC. Our RNA-based classifier identified enrichment in adaptive immunity in AR-low compared to AR-high ER-negative tumors.
Previous studies have not evaluated associations between AR and specific DNA repair pathways. We observed a higher prevalence of homologous recombination deficiency in AR-low (versus AR-positive) ER-negative-breast cancer. This finding is consistent with previous studies showing increased genomic instability in AR-negative (versus AR-positive) TNBC. It has been discovered that AR-negative TNBCs have 1) increased epidermal growth factor receptor, cyclin-dependent kinase 6, Ki-67, and topoisomerase 2a but 2) downregulated PTEN and HER4[50–53]. It was also discovered that AR-negative tumors display a higher level of copy number alterations (CNAs), CIN25, centrosome amplification, and miRNAs/mRNAs pairings associated with genomic instability, cell cycle, and DNA damage[54]. Thus, AR-negativity in TNBC may be linked to dysregulation in the cell cycle and impaired DNA damage response, specifically homologous recombination.
A limitation of this study was the small number of ER-negative breast cancers, particularly TNBC. We also did not evaluate protein-level AR localization compared to our multigene classifier. However previous studies show that AR RNA-based signatures expression correlate with AR protein expression[55, 56]. However, our results suggest that RNA-based methods may be a valuable tool to identify AR-low ER-negative breast cancer and may further our understanding of the unique tumor biology associated with AR-low status among ER-negative breast cancers.