Cancer arises DNA mutations, which lead to diverse changes ranging from single nucleotide alterations to chromosome rearrangement, fostering tumor diversity. The APOBEC family deaminates cytosine in DNA and RNA, leading to somatic mutations, DNA breaks, RNA modifications, or DNA demethylation (Figure 2). This activity serves as mutagenic fuel for cancer evolution and heterogeneity (Swanton et al., 2015), particularly in bladder and breast cancers (Middlebrooks et al., 2016; Swanton et al., 2015; Burns et al., 2013b; Alexandrov et al., 2013; Roberts et al., 2013).

Previous studies have identified over 30 SBSs (single-base substitutions) signatures in malignant tumors, with SBS2 and SBS13 attributed to APOBEC activity (Alexandrov et al., 2020). APOBEC3 may diversify extrachromosomal oncoproteins and promote the evolution of ecDNA-containing tumors by mutagenesis of ecDNA, exploiting its cyclic nature, and repeated mutations (Bergstrom et al., 2022). Notably, 59.2% of hypermutated breast cancers exhibit a dominant APOBEC mutational signature, while 36.4% show a dominant mismatch repair-deficient (dMMR) signature (Barroso-Sousa et al., 2020), which is a significant mechanism related to hyper-mutation. In particular, breast cancer patients with APOBEC-rich features exhibit higher mutational loads and APOBEC3B protein levels compared to other tumors (Krug et al., 2020), and A3B is also associated with a hypermutated phenotype (Roberts and Gordenin, 2014). Additionally, SBS2 and SBS13 mutations are also enriched in metastatic caners. Martínez-Jiménez et al. revealed that APOBEC mutation burden significantly increases in six metastatic tumor types (breast, colorectal, stomach, kidney, prostate and pancreatic neuroendocrine carcinomas) (Martínez-Jiménez et al., 2023). Compared to early breast cancer, HR+/HER2− metastatic breast cancer shows an increasing trend in SBS2 and SBS13 signatures. The APOBEC mutational signature S13 increases significantly during the transition from the luminal A subtype to the more aggressive luminal B and HER2-enriched subtypes (Park et al., 2023), correlating with poor outcome and resistance to endocrine therapy (Bertucci et al., 2019). APOBEC signatures are also observed in the late stages of breast cancer evolution (Nik-Zainal et al., 2016). Furthermore, most TMB-high breast metastatic invasive lobular carcinoma (mILCs) harbor an APOBEC trinucleotide signature (14/16; 88%) (Sokol et al., 2019). APOBEC activity varies across breast cancer subtypes, with typically higher activity observed in triple-negative breast cancer (TNBC), potentially contributing to its malignant transformation and progression (Petljak et al., 2022b). In conclusion, APOBEC is strongly associated with cancer occurrence and evolution.

Burns et al. quantified mRNA levels of APOBEC family members in 38 independent breast cancer cell lines and found that only A3B mRNA was upregulated in most cell lines (28/38) (Burns et al., 2013a). Furthermore, upregulation of A3B and high uracil load resulted in 3–5 times more mutations. In addition, inactivation of TP53 is a prerequisite for bypassing DNA damage checkpoints caused by A3B. Likewise, Periyasamy et al. investigated the regulation of A3B gene expression and illuminated negative correlation between A3B expression with p53 (protein expressed by TP53). It occurs through induction of p21 (CDKN1A) and recruitment of repressive DREAM complex to A3B gene promoter, so that mutation of p53 represses the recruitment and leads to upregulation of A3B (Periyasamy et al., 2017). On the other hand, upregulated APOBEC is connected with high level of PD-L1 expression (Boichard et al., 2017). Proteogenomic studies have shown that APOBEC features promote an active immune microenvironment associated with PD-L1 mRNA expression, particularly in luminal breast cancer subtypes (Ohtsubo et al., 2017). Thus, APOBEC-mediated mutations may facilitate immune escape in cancer cells. Conversely, in breast cancer patients with somatic BRCA1/2 mutations, APOBEC-mediated mutations may be passenger mutations, particularly when the BRCA1/2 mutations have limited functional impact. For instance, APOBEC activity does not correlate with PARP inhibitor sensitivity, suggesting that APOBEC is not always a primary driver of tumor growth (Vidula et al., 2020).

Furthermore, Venkatesan et al. investigated when APOBEC3 expression is induced during cancer development. APOBEC3 protein expression peaks in the pre-invasive stage of breast cancer and occurs early in non-small cell lung cancer (NSCLC) evolution. This can be explained by DNA replication stress inducing APOBEC3 mutations, which drive the early onset of carcinoma in situ (CIN) and accelerate the deletion of tumor suppressor genes (TSGs) (Venkatesan et al., 2021).

A3A induces a unique replication stress that sensitizes breast cancer cells to ataxia telangiectasia and Rad3-related kinase inhibitors (ATRi) but not to other replication inhibitors or DNA-damaging agents (Buisson et al., 2017; Buisson et al., 2019). ATR is a phosphoinositide 3-kinase-related protein kinase (Bentley et al., 1996), which responds to DNA double-strand breaks by coordinating replication stress, thereby maintaining genome integrity. Cancer cells have higher levels of replication stress and greater dependence on ATR, making ATRi a promising strategy for sensitizing cancer cells to DNA repair and replication-targeted therapies (Saldivar et al., 2017). Hyunho Kim et al. demonstrated that combining an ATR inhibitor with cisplatin yields promising results in treating muscle-invasive bladder cancer (MIBC) cells with high APOBEC3B expression (Kim et al., 2024). Enrichment of high TMB in mILCs, most of which harbor APOBEC signatures, has been identified as a significant determinant of response to ICI (Rizvi et al., 2015; Blank and Enk, 2015; Philips and Atkins, 2015). A large study of mutational processes in breast cancer suggested that APOBEC is a key driver of hypermutation in metastatic tumors. High TMB may benefit the use of ICIs in various cancers, including small cell lung cancer, where APOBEC enrichment may improve outcomes after immunotherapy (Wang et al., 2018). Preliminary evidence also suggests potential benefits of ICIs in breast cancer patients with enriched APOBEC features (Barroso-Sousa et al., 2020). Saranya Chumsri et al. reported that a case of PD-L1 and HER2 negative advanced breast cancer with high TMB and APOBEC features, previously considered immunologically cold, that benefited from long-term ICI therapy. Andrew A. Davis et al. demonstrated that APOBEC, as a potential biomarker in patients with blood TMB (bTMB), can identify patient groups likely to benefit from ICI treatment (Davis et al., 2023). In addition, a similar proportion of high TMB cases with APOBEC features was observed across distinct breast cancer subtypes (Chumsri et al., 2020). In a study using next-generation sequencing (NGS) for circulating tumor DNA (ctDNA) analysis, APOBEC was verified to be enriched in both high bTMB and low bTMB HR+/HER2− patients, further validating that APOBEC can be used as a biomarker by testing blood to predict response to ICI therapy and to decide whether to combine ICI with chemotherapy (Davis et al., 2023). Therefore, we propose that APOBEC mutation characteristics and TMB may serve as predictors of clinical outcome and response to ICI therapy in breast cancer patients, particularly in advanced breast cancer.

An alternative perspective posits that APOBEC activity fosters an immunologically hot tumor microenvironment, triggering antigen-specific adaptive immunity mediated by CD4⁺ T cells. This process enhances immune cell infiltration and slows tumor growth (Cescon et al., 2015; Smid et al., 2016; Chen et al., 2019). Therefore, DiMarco AV et al. explored the role of CD4⁺ T cells in anti-tumor immunity and their relationship with APOBEC, particularly in HER2-driven breast cancer (DiMarco et al., 2022). They proposed the idea of CTLA-4 inhibitors or CD4⁺ T cell adoptive transfer for patients with high APOBEC features and demonstrated that APOBEC enhances sensitivity to anti-CTLA-4 combined with anti-HER2 therapy (DiMarco et al., 2022). Nicola Cosgrove et al. found a higher prevalence of APOBEC-related mutational signatures in HER2-positive tumors, particularly the ER negative/HER2 positive subtype, correlating with increased immune cell infiltration and pathological complete response (pCR) (Cosgrove et al., 2023). However, this implies that tumors must exploit the immunogenicity generated by APOBEC for targeted therapy, rather than progressing due to high mutational burden. Thus, APOBEC is a double-edged sword: it promotes immunogenicity and anti-tumor immunity while also inducing genetic heterogeneity, subclonal diversity, and immune evasion. Therefore, APOBEC mutational features and mutant clonality hold promise as biomarkers for predicting immunotherapeutic response.

In HR positive/HER2 negative metastatic breast cancer, combining CDK4/6 inhibitors with endocrine therapy (ET) is an effective treatment, but drug resistance remains a significant challenge. Elevated APOBEC mutational signature S13 often correlates with genomic instability and acquired drug resistance, including RB1 inactivation, which confers resistance to CDK4/6 inhibitors like palbociclib (Park et al., 2023).

During tumor progression, in addition to different mutational signatures, tumors also acquire drug resistance to conventional treatments. In a study of circulating tumor DNA (ctDNA) genomic profiles in advanced breast cancer, it has been demonstrated that subclonal mutations in HR-positive and HER2-negative breast cancers were enriched for APOBEC signatures and are continuously activated during endocrine therapy to modify PIK3CA (Law et al., 2016), generating frequent secondary hits of new mutations that upregulate PI3K signaling (Kingston et al., 2021). Given the crosstalk between ER and PI3K signaling pathways, PI3K inhibition increases ER-dependent transcription, leading to endocrine therapy resistance (Juric et al., 2015). Therefore, early combination of APOBEC or PI3K inhibitors with endocrine therapy may improve outcomes. In ER positive breast cancer, high expression of A3B was also associated with unfavorable clinical parameters (Sieuwerts et al., 2014). Subsequently, a study revealed that tumors harboring multiple PIK3CA mutations were associated with higher TMB and APOBEC mutation profiles (Sivakumar et al., 2023). The combination of Alpelisib (an orally PI3K inhibitor) and fulvestrant significantly improves progression-free survival (PFS) in patients with metastatic HR+ breast cancer, with adverse events that are manageable and well-tolerated (André et al., 2021).

Moreover, in non-small cell lung cancer (NSCLC), the commonly treatment with tyrosine kinase inhibitors (TKIs) can induce drug-tolerant persisters (DTPs) that highly express APOBEC3A, promoting genomic instability and the evolution of drug-resistant mutations. Thus, in turn, it induces the evolution of drug-resistant mutations in cancer cells (Isozaki et al., 2023).

APOBEC activity serves as a potential predictor of both treatment response and survival in breast cancer patients. In the HR-positive subgroup, APOBEC mutation signatures are associated with increased pathological complete response (pCR) following neoadjuvant chemotherapy (Denkert et al., 2021). However, in HR-positive and HER2-negative breast cancers, APOBEC mutational signatures correlate with poor outcomes with CDK4/6 inhibitors and endocrine therapy (Sammons et al., 2022). In addition, APOBEC is also associated with increased Ki-67 and tumor-infiltrating lymphocytes (TILs) levels, implying more aggressive tumor progression but also increased immunogenicity. This dual effect improves chemotherapy response rate (Figure 3). In conclusion, APOBEC signatures enhance chemotherapy response rates and pCR in HR-positive breast cancer but reduce the benefit of targeted therapy (Fulton-Ward and Middleton, 2023).

The correlation between APOBEC activity and high mutational load implies that APOBEC-driven mutations facilitate the disorganization of cancer cell genomes, promoting their evolution toward a more aggressive phenotype. This process is a hallmark of tumor heterogeneity. However, as previously discussed, APOBEC activity also enables tumors to thrive in an immunologically hot environment, essential for immunotherapy efficacy. This is because immunotherapy relies on the production of tumor neoantigens to elicit a robust immune response.

One study has proposed the potential for inducing APOBEC-driven mutations through first-line therapies, such as oncolytic virus therapy, and subsequently selecting cancer cells with a specific phenotype for targeted treatment. In vitro experiments shown that transfecting tumor cells with APOBEC expression vectors can induce APOBEC-mediated mutations, generating new epitopes that stimulate T cells. This approach, known as heteroclitic epitope-activated therapy (HEAT), leverages APOBEC-induced mutations to enhance immunogenicity and drive anti-tumor immunity. Alternatively, associating mutational signature acquisition with in situ tumor killing can sensitize tumors to immune checkpoint blockade therapy, a strategy referred to as hypermutagenic immunotherapy (HIT) (Vile et al., 2021).

Nevertheless, in NSCLC, TKIs have been shown to induce high APOBEC3A expression, promoting genomic instability. While this allows drug-tolerant persisters (DTPs) to survive longer and gain a survival advantage, it also highlights the complex interplay between APOBEC activity and therapeutic outcomes (Vile et al., 2021).

In summary, the clinical significance and therapeutic potential of APOBEC activity present contrasting perspectives. On one hand, APOBEC-driven mutations can enhance immunogenicity and improve immunotherapy efficacy. On the other hand, they can promote genomic instability and resistance to targeted therapies. Collectively, future research is urgently needed to develop APOBEC inhibitors and inducers that can be harnessed for medical purposes, thereby optimizing the therapeutic landscape for cancer treatment.