Abstract P3-09-13: Androgen receptor loss is associated with genomic instability characterized by copy number alterations and mirna deregulation in triple-negative breast cancer

Abstract

Abstract Background: Triple-negative breast cancer (TNBC) comprises 10%-20% of invasive breast carcinoma cases. Patients with TNBC exhibit poorer 5-year survival and higher rates of metastasis and recurrence than patients with other breast cancer subtypes. TNBC is further divided based on gene expression profiling into androgen receptor (AR)-positive (AR+) TNBC and AR-negative TNBC (or quadruple-negative breast cancer [QNBC]). While AR is an emerging therapeutic target for AR+ TNBC, there are no treatment options for QNBC. AR expression is associated with favorable disease-free, overall, and recurrence-free survival in patients with TNBC, suggesting that AR loss in TNBC tumors confers an aggressive disease course. Genomic instability has been recognized as one of the drivers of tumorigenesis and can be evidenced by the presence of chromosomal instability, such as DNA copy number alterations (CNAs). Although there are many studies characterizing the genomic profiles of TNBCs, little is known about the tumor biology and genetic makeup of QNBCs. In this study, we explored the impact of CNAs on microRNA (miRNA) expression and, subsequently, on signaling pathways associated with QNBC aggressiveness and clinical outcomes. Methods: AR expression was immunohistochemically assessed in tissues of 53 patients with TNBC from the Histopathology and Tissue Shared Resources of Georgetown University. AR positivity was defined as AR expression in >1% of cells. Genome-wide copy number profiling of formalin-fixed paraffin-embedded samples was performed using the Agilent SurePrint G3 Human CGH Microarray, and miRNA expression analysis was conducted using NanoString nCounter Human v3a miRNA Expression Assay. Differentially expressed miRNAs between TNBC and. QNBC samples were integrated with array CGH data from the same tissue sample to identify common gene targets that may be affected by both CNAs and miRNA deregulation. Functional enrichment analysis was performed to identify cancer pathways deregulated in QNBC. The expression levels of Centrosome Amplification 20 (CA20) and Chromosome Instability 25 (CIN 25) gene signatures were evaluated in 524 primary invasive breast cancers from The Cancer Genome Atlas (TCGA) database. Results: We observed that 64% of TNBC samples lacked AR expression and that QNBCs exhibited a significantly higher CNA level (p<0.05) and frequency (p<0.0001) compared with TNBCs. Gains at 1q21-q44, 6p25.3-p12.1, 8q11.1-q24.3, 9p24.3-p13.1, 10p15.3-p11.1, and 12p13.33-p11.1 were common CNAs observed in >50% of QNBCs. Additionally, CNAs affecting genes of the CIN25 signature were significantly higher in QNBC than in TNBC; however, CNAs in CA20 signature genes were similar in QNBC and TNBC samples. Notably, the expression levels of CA20 and CIN25 genes were significantly higher in QNBC than in TNBC. Moreover, we identified 184 differentially expressed miRNAs between QNBC and TNBC samples (p<0.05, FDR<0.25). Among these miRNAs, 15 were mapped at cytobands with CNAs, and eight (miR-23c, miR-548ai, miR-567, miR-613, miR-943, miR-1204, miR-1265, and miR-1267) presented concordance between their expression levels and CNAs. The target genes of these eight miRNAs were associated with genomic instability, cell cycle, and DNA damage response. Importantly, the combined expression levels of these eight miRNAs robustly discriminated between TNBCs and QNBCs with an area under the curve of 0.946. Conclusions: Our study highlights that loss of AR expression in TNBC is associated with profound genomic instability as evidenced by CNAs and deregulation of miRNA expression, which leads to upregulation of signaling pathways associated with cancer aggressiveness. Citation Format: Shristi Bhattarai, Bruna M. Sugita, Luciane Cavalli, Ritu Aneja. Androgen receptor loss is associated with genomic instability characterized by copy number alterations and mirna deregulation in triple-negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-09-13.