Abstract P4-04-04: APOBEC3F is expressed by immune cells and is associated with immune response and survival in triple negative breast cancer
Authors: Wu Rongrong , Oshi Masanori , Asaoka Mariko , Yamada Akimitsu , Yan Li , Endo Itaru , Ishikawa Takashi , Takabe Kazuaki 
Published: March 2022

Background: The Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) cytidine deaminases subfamily has been a focus of attention as a cause of characteristic somatic mutations in breast cancer. APOBEC3A and APOBEC3B are known to be the key mutation drivers in breast cancer, while the other APOBEC3 family members have been implicated in infection. APOBEC3F was reported to inhibit HIV replication, but its role in cancer has not been reported. We hypothesized that APOBEC3F is associated with infiltrating immune cells and immune responses in tumor microenvironment, and with survival of breast cancer patients. Method: We analyzed a total of 2978 breast cancer patients’ clinical data and transcriptome from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and The Cancer Genome Atlas (TCGA) datasets. We also used a total of 21802 single-cell transcriptomes from the GSE75688 and GSE114725 single-cell sequencing datasets of the primary breast cancer cohort. We defined "high expression" as top two thirds of APOBEC3F expression in each cohort. Result: APOBEC3F expression was significantly high in triple negative (TNBC), which is known to have the most abundant immune cell infiltration among the subtypes. Disease-specific survival (DSS) and overall survival (OS) were consistently better in high APOBEC3F TNBC (all p &lt; 0.05), but not in luminal subtype, that led us to hypothesize that APOBEC3F may enhance cancer immunity. APOBEC3F expression was not consistently associated with intratumor heterogeneity, mutation rates nor neoantigens that are all reflections of cancer cells in both TNBC and luminal breast cancer, except for HRD in TNBC (p = 0.024). APOBEC3F expression did not correlate with response to any of the drugs tested in breast cancer cell lines in vitro. On the other hand, APOBEC3F expression was consistently associated with multiple types of immune cell infiltrations, such as CD8+ T-cells, M1 and M2 macrophage, Dendritic cells, Natural Killer cells (NK), and B-cells (all p &lt; 0.05) with high CYT (p &lt; 0.001) regardless of subtype. In TNBC, high APOBEC3F tumor significantly enriched only immune-related gene sets; inflammatory response, IL-2/STAT5 signaling, IFN γ response, IFN α response,IL-6/JAC/STAT3 signaling and complement, consistently in both cohorts, and associated with high levels of immune activity scores such as IFN-γ response, tumor infiltrating lymphocytes regional fraction, lymphocyte infiltration signature, leukocyte fraction, and TCR richness in TCGA cohort (all p &lt; 0.05). In luminal breast cancer, high APOBEC3F tumor significantly enriched not only immune-related gene sets similar to TNBC, but also tumor aggravating gene sets such as KRAS signaling, PI3K signaling, angiogenesis, metabolism-related gene sets, as well as apoptosis-related gene sets. We further found that APOBEC3F was exclusively expressed in immune cells compared to myeloid, stromal, and cancer cells using the GSE75688 breast cancer single cell sequencing cohort, and highly expressed in CD8, CD4, NK, and B-cells, and neutrophils in GSE114725 breast cancer single cell sequencing cohort (both p &lt; 0.001). High APOBEC3F immune cells were significantly associated with higher expression of IFN-γ, cytolytic activity score and its component genes, and with immune cell proliferation (all p &lt; 0.001). High APOBEC3F tumor was associated with significantly elevated levels of all the immune checkpoint molecules tested (all p &lt; 0.001). Conclusion: Our study demonstrated that high APOBEC3F gene expression is exclusively expressed in immune cells and is associated with immune response, immune cytolytic activity in the tumor microenvironment, and with favorable survival in triple-negative breast cancer using in silico bioinformatic analyses of multiple independent large patient cohorts.

Citation Format: Rongrong Wu, Masanori Oshi, Mariko Asaoka, Akimitsu Yamada, Li Yan, Itaru Endo, Takashi Ishikawa, Kazuaki Takabe. APOBEC3F is expressed by immune cells and is associated with immune response and survival 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 P4-04-04.