The APOBEC family of cytidine deaminases is one of the most common endogenous sources of mutations in human cancer. Genomic studies of tumors have found that APOBEC mutational signatures are particularly enriched in the HER2 subtype of breast cancer and have been associated with immunotherapy response in diverse cancer types. However, the direct consequences of APOBEC mutagenesis on the tumor immune microenvironment have not been thoroughly investigated. To address this, we developed syngeneic murine mammary tumor models with inducible expression of APOBEC3B. We found that APOBEC activity induces an antitumor adaptive immune response and CD4+ T cell-mediated tumor growth inhibition. While polyclonal APOBEC tumors had a moderate growth defect, clonal APOBEC tumors were almost completely rejected by the immune system, suggesting that APOBEC-mediated genetic heterogeneity limits the antitumor adaptive immune response. Consistent with the observed immune infiltration in APOBEC tumors, APOBEC activity sensitized HER2-driven breast tumors to checkpoint inhibition. In human breast cancers, the relationship between APOBEC mutagenesis and immunogenicity varied by breast cancer subtype and the frequency of subclonal mutations. This work provides a mechanistic basis for the sensitivity of APOBEC tumors to checkpoint inhibitors and suggests a rationale for using APOBEC mutational signatures as a biomarker predicting immunotherapy response in HER2-positive breast cancers.

Purpose Androgen receptor (AR) expression is absent in 40–90% of estrogen receptor (ER)-negative breast cancers. The prognostic value of AR in ER-negative patients and therapeutic targets for patients absent in AR remains poorly explored. Methods We used an RNA-based multigene classifier to identify AR-low and AR-high ER-negative participants in the Carolina Breast Cancer Study (CBCS; N = 669) and The Cancer Genome Atlas (TCGA; N = 237). We compared AR-defined subgroups by demographics, tumor characteristics, and established molecular signatures [PAM50 risk of recurrence (ROR), homologous recombination deficiency (HRD), and immune response]. Results AR-low tumors were more prevalent among younger (RFD =  + 10%, 95% CI = 4% to 16%) participants in CBCS and were associated with HER2 negativity (RFD = − 35%, 95% CI = − 44% to − 26%), higher grade (RFD =  + 17%, 95% CI = 8% to 26%), and higher risk of recurrence scores (RFD =  + 22%, 95% CI = 16.1% to 28%), with similar results in TCGA. The AR-low subgroup was strongly associated with HRD in CBCS (RFD =  + 33.3%, 95% CI = 23.8% to 43.2%) and TCGA (RFD =  + 41.5%, 95% CI = 34.0% to 48.6%). In CBCS, AR-low tumors had high adaptive immune marker expression. Conclusion Multigene, RNA-based low AR expression is associated with aggressive disease characteristics as well as DNA repair defects and immune phenotypes, suggesting plausible precision therapies for AR-low, ER-negative patients.

Background: Black and younger women have poorer breast cancer outcomes. Using a diverse population-based study, we examined the role of biology as measured by genomic assays in outcome disparity among clinically HR+/HER2- women. Methods: Data and biospecimens from the Carolina Breast Cancer Study (CBCS, including 2,103 non-metastatic, invasive breast cancers) were used to perform RNA-based classification according to molecular subtype and research versions of known prognostic assays, the 21-gene Recurrence Score (RS) and the PAM50-based Risk of Recurrence (ROR-PT) score. Prevalence odds ratios (PORs) and 95% confidence intervals (CIs) for subtype by race and age were estimated. Results: Black women had higher frequency of Luminal B [POR (95% CI): 2.08 (1.60, 2.71)], HER2-enriched [POR (95% CI): 2.01 (1.45, 2.79)], and Basal-like tumors [POR (95% CI): 3.51 (2.81, 4.40)] compared to non-Black women. Similarly, younger (< 50 years) women had higher frequency of Luminal B [POR (95% CI): 1.57 (1.21, 2.04)], HER2-enriched [POR (95% CI): 2.03 (1.46, 2.82)], and Basal-like tumors [POR (95% CI): 2.40 (1.92, 3.01)]. Additionally, within clinically-defined HR+/HER2- tumors, Black women had higher frequency of high ROR-PT among younger women [POR (95% CI): 2.88 (1.19, 6.97)], but this association was attenuated among older women [POR (95% CI): 1.99 (0.84, 4.71)]. Race was not significantly associated with the 21-gene RS among younger or older women. Conclusion: While Black and younger women with clinically-defined HR+/HER2- often have higher burden of non-Luminal/high genomic risk tumors, PAM50 and 21-gene assays show different demographic patterns and heterogeneity within age- and race-defined groups, underscoring the value of genomic testing in understanding outcome disparities. Citation Format: Sanah Vohra, Sarah Van Alsten, Joannie M. Ivory, Alina Hamilton, Xiaohua Gao, Erin Kirk, Joseph Nsonwu-Farley, Ebonee Butler, Brianna Taffe, Charles M. Perou, Lisa Carey, Melissa Troester. PAM50 and 21-gene recurrence scores in younger and Black women with breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD1-08.

Purpose: Androgen receptor (AR) expression is absent in 40-90% of estrogen receptor (ER)-negative breast cancers. The prognostic value of AR in ER-negative patients and therapeutic targets for patients absent in AR remains poorly explored. Methods: We used an RNA-based multigene classifier to identify AR-low and AR-high ER-negative participants in the Carolina Breast Cancer Study (CBCS; n=669) and The Cancer Genome Atlas (TCGA; n=237). We compared AR-defined subgroups by demographics, tumor characteristics, and established molecular signatures [PAM50 risk of recurrence (ROR), homologous recombination deficiency (HRD), and immune response]. Results: AR-low tumors were more prevalent among Black (relative frequency difference (RFD) = +7%, 95% CI = 1% to 14%) and younger (RFD = +10%, 95% CI = 4% to 16%) participants in CBCS and were associated with HER2-negativity (RFD = -35%, 95% CI = -44% to -26%), higher grade (RFD = +17%, 95% CI = 8% to 26%), and higher risk of recurrence scores (RFD = +22%, 95% CI = 16.1% to 28%), with similar results in TCGA. The AR-low subgroup was strongly associated with HRD in CBCS (RFD = +33.3%, 95% CI = 23.8% to 43.2%) and TCGA (RFD = +41.5%, 95% CI = 34.0% to 48.6%). In CBCS, AR-low tumors had high adaptive immune marker expression. Conclusion: Multigene, RNA-based low AR expression is associated with aggressive disease characteristics as well as DNA repair defects and immune phenotypes, suggesting plausible precision therapies for AR-low, ER-negative patients.