ESR1 fusions in breast cancer: functions, mechanisms and therapeutic opportunities

Introduction

Breast cancer is the most common malignant disease in women worldwide. The lifetime risk of developing breast cancer for a woman is approximately 13%. The disease is estimated to cause the death of over 42,000 women in the US in 2025 (American Cancer Society).

Breast cancer displays high heterogeneity. According to protein tumor markers, such as estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2) and progesterone receptor (PR), it is commonly classified into three clinical subtypes, including ER⁺, HER2⁺ and triple negative (ER⁻, HER2⁻, PR⁻), which guide therapeutic selection. The analysis of gene expression by Prediction Analysis of Microarray of a 50-gene set (PAM 50) has further categorized the disease into five intrinsic molecular subtypes, including luminal A (ER⁺, HER2⁻), luminal B (ER⁺, HER2⁻/⁺), HER2-enriched (ER⁻, PR⁻, HER2⁺), basal-like (ER⁻, HER2⁻, PR⁻) and normal-like (1,2). The stratification of intrinsic subtypes is strongly informative of prognosis (2,3).

The majority of breast cancers express estrogen receptor-alpha (ERα) that is activated by estrogen binding, driving tumor growth and disease progression. ERα is encoded by the gene, ESR1. ERα contains several functional domains, including the N-terminal activation function 1 (AF1) domain, DNA-binding domain (DBD), the hinge region, and C-terminal activation function 2/ligand-binding domain (AF2/LBD) (Figure 1A). The AF1 domain is subject to post-translational modifications, such as phosphorylation at multiple serines, and interacts with coactivators (CoAs), such as steroid receptor coactivators (SRC)-1, SRC-2, and SRC-3 and steroid receptor RNA activator (4-9). The DBD is composed of two zinc fingers and binds to palindromic estrogen response element (ERE) sequences located within regulatory regions of ERα target genes (10). The AF2/LBD domain binds estrogenic agonist ligands, including the predominant female estrogen, 17ꞵ-estradiol (E2).

Figure 1 Wild-type ERα, ESR1 LBD mutants, and ESR1-e6 fusions signaling in breast cancer. (A) The wild-type ESR1 gene encodes the ERα protein that is activated by estrogen binding, leading to dimerization, binding to estrogen response elements in target genes, and recruitment of transcriptional CoAs to drive gene transcription and tumor growth. ETs inhibit this process by blocking or degrading ERα or synthesis of estrogen. (B,C) ESR1 alterations promote ET resistance and metastasis. (B) Point mutations in the last exon of ESR1 that encodes the LBD produce constitutively active, ligand-independent ERα proteins that drive estrogen-responsive and metastatic transcriptional programs. New FDA-approved oral SERDs are more potent in inhibiting these mutant ERα proteins. (C) ESR1 fusions replace the LBD with diverse 3' gene partners, allowing for the expression of chimeric in-frame fusion proteins. These fusions activate similar transcriptional programs as the ERα point mutants, but unlike the point mutants, these fusions are fully resistant to ETs. CDK4/6i reduce growth of ESR1 fusion-driven tumors, but without tumor eradication, highlighting the need for additional targeted therapy. Key: first two exons in white are untranslated exons of ESR1 mRNA. AF, activation function; CDK4/6i, CDK4/6 inhibitor; CoA, transcriptional coactivator; DBD, DNA-binding domain; EMT, epithelial-to-mesenchymal transition; ERα, estrogen receptor-alpha; ETs, endocrine therapies; FDA, Food and Drug Administration; H, Hinge region; LBD, ligand-binding domain; SERDs, selective estrogen receptor degraders.

In the nucleus, upon agonist-binding, ERα undergoes a conformational change in its LBD that provides the interface for binding of CoAs to form an active transcriptional complex (4,11). The LBD also binds ERα antagonists, such as endocrine therapy (ET) drugs, but with an altered conformation compared to agonists (11). The hinge region contains the nuclear localization signal and mediates the synergistic function of AF1 and AF2, allowing full transcriptional activity of ERα in response to agonistic ligands (12) (Figure 1A). ERα also acts in a non-canonical pathway to tether to other transcriptional factors (TFs), such as activator protein 1 (AP-1) and specificity protein 1 (Sp1) at their target genes, thereby modulating gene transcription (13,14). In contrast to the two above genomic pathways of nuclear ERα, E2-liganded ERα can function through a “non-genomic” signaling pathway (15). The crosstalk of ER with receptor tyrosine kinases (RTKs) including epidermal growth factor receptor (EGFR), HER2, and insulin-like growth factor receptor (IGF1R) activates downstream kinases that then can phosphorylate multiple TFs and CoAs to induce gene expression (16-18).

ET drugs are the mainstay treatments for ERα⁺ breast cancer, including aromatase inhibitors (AIs) that block the production of E2 (19), selective estrogen receptor modulators (SERMs) such as tamoxifen (20), which block ERα function (21), and selective estrogen receptor degraders (SERDs) such as fulvestrant, which induces degradation of ERα (22). Luteinizing hormone-releasing hormone agonist (LH-RHa) agents reduce estrogen levels in women by inhibiting the pituitary gland. ET drugs are effective in the treatment of early/advanced breast cancer in premenopausal women (23,24). These agents are highly effective against wild-type (WT) ERα, with some efficacy against ESR1 LBD point mutants but no inhibition of ESR1 fusion proteins that are expressed in metastatic, postmenopausal patients. Despite the efficiency of ET, many patients eventually have disease progression due to acquired drug resistance with the development of lethal metastasis after an initial favorable response. Therefore, it is critical to better understand the underlying mechanisms and therapeutic strategies to treat ET-refractory, ERα⁺ metastatic breast cancer (MBC).

One well-studied mechanism of acquired ET resistance is due to point mutations in the last exon of ESR1 encoding the LBD, identified in up to 40% of ERα⁺ MBC but rarely found in primary breast tumors (25-29). D538G and Y537S are the most recurrent ERα point mutants in metastatic disease. These mutations drive constitutive E2-independent activation of ERα target genes and enhance cell proliferation (Figure 1B) (25-29). The formation of hydrogen bonds between S537 or G538 and D351 contributes to the agonist conformation of these ERα mutants (26,30). Although ESR1 LBD mutant tumors demonstrated resistance to AI therapy, they are sensitive to inhibition by fulvestrant and two FDA-approved oral SERDs (26,28,31-33). Given the high prevalence of ESR1 LBD mutations in ET resistance, they have been extensively reviewed elsewhere (29,34,35). A more recently recognized recurrent mechanism of ET resistance involves chromosomal rearrangements in the ESR1 gene that generate chimeric fusion proteins in which the ESR1 LBD is replaced by heterogeneous 3' partner sequences (Figure 1C). This review focuses on these ESR1 fusions, summarizing their prevalence in MBC, association with ET resistance, underlying mechanisms, therapeutic vulnerabilities, and remaining unanswered questions.

Gene fusions as oncogenic drivers

Gene fusions generated from chromosomal rearrangements are recognized as key drivers of oncogenesis. In addition to well-described gene fusion-driven hematological malignancies (36,37), their roles in solid tumors are now being recognized. The IGH-MYC fusion in Burkitt’s lymphoma (37) drives aberrant expression of the partner oncogene MYC, causing disease pathogenesis. Similarly, the oncogenic TMPRSS-ERG fusion, found in 50% of prostate cancer cases, causes deregulated expression of the ETS domain-containing TF ERG (38). Beyond altered oncogenic expression, chromosomal rearrangements can also produce chimeric pathogenic fusion proteins, such as BCR-ABL in chronic myeloid leukemia (39) and EML4-ALK in lung cancer (40). Hence, gene fusions represent a fundamental mechanism of oncogenic activation across cancers, emphasizing the importance of investigating their roles in breast cancer.

Fusions in different breast cancer subtypes

Among the different subtypes of breast cancer, gene fusions resulting from chromosomal translocations are most observed in triple-negative breast cancer (TNBC), followed by HER2-positive tumors—subtypes known for their aggressive phenotypes and greater genomic instability compared to ER⁺ tumors (41-43). Within ER⁺ breast cancers, luminal B tumors exhibit a higher frequency of gene fusions than the less aggressive luminal A subtype (41-43).

ESR1 fusions in primary tumors

We screened approximately 1,200 primary breast cancer patients in The Cancer Genome Atlas (TCGA) (44) using TAR-Fusion prediction in the ChimerDB 4.0 dataset (45) and identified 27 fusions involving the ESR1 gene, occurring at ~2% frequency. The majority had ESR1 as the 5' partner gene while only two had ESR1 as the 3' partner, fused to AKAP7 at 5'. The most common fusions identified were ESR1-CCDC170 and ESR1-AKAP12.

As the most recurrent ESR1 fusion in primary breast cancer, ESR1-CCDC170 was first reported in luminal B breast tumors and biologically characterized by Veeraraghavan et al. (46). The CCDC170 (coiled-coil domain containing 170) gene is located immediately adjacent to ESR1 on chromosome 6 and encodes a protein involved in the organization and stabilization of microtubules. This “promoter switching” fusion preserves the first two non-coding exons of the ESR1 gene and upstream ESR1 promoters that become fused to different exons of the neighboring CCDC170 gene. This action produces truncated CCDC170 proteins of different sizes without retaining any part of the ERα protein. These altered CCDC170 proteins drive ET-resistant tumor growth in experimental models (46).

In a large cohort of advanced breast cancer patients, Heeke et al. (47) identified 40 unique ESR1 fusion partners, with CCDC170 being the most frequent out-of-frame partner (n=17), followed by ARMT1 (n=3). ESR1-CCDC170 fusions mainly involved ESR1 exon 2 (ESR1-e2) and CCDC170 exon 2, though other ESR1 gene breakpoints (exons 3–7) were also observed (47). In contrast, Vitale et al. (48) found ESR1-e2 fused to CCDC170 exon 8 to be the most frequent variant in primary tumors. They also report this specific variant to be associated with lower overall survival, identifying it as a clinically relevant event in primary ER⁺ breast cancer.

Among the different variants of ESR1-CCDC170 fusions, only five produce a stable CCDC170 protein and retain its key ATP binding pocket (42). While some reports, such as Vitale et al. (48), detected the ESR1-CCDC170 fusion in both normal and metastatic tumors, other studies, like Veeraraghavan et al. (46), did not detect the fusion in normal breast tissues. Given that ESR1-CCDC170 is currently the only ESR1 fusion found in primary ER⁺ breast tumors with demonstrated promotion of ET resistance, these discrepancies require further investigation. ESR1-CCDC170 fusions activate HER2 signaling by CCDC170 proteins binding to HER2/HER3/SRC complexes and promoting AKT survival pathways, allowing the cells to bypass E2-dependence (42,49). As a result, tumors expressing this fusion may be sensitive to anti-HER2 therapies (42,49). Consistent with this, ESR1-CCDC170 was detected in a treatment-naive tumor of an ER⁺/HER2⁺ metastatic patient (50), supporting its role in HER2 signaling activation.

The most recurrent ESR1 fusions detected in primary ER⁺ breast tumors, ESR1-CCDC170, ESR1-AKAP12, and ESR1-ARMT1 (also known as ESR1-C6orf211), originate from intra-chromosomal rearrangements and were initially found in patients with ET-resistant disease, suggesting a role of these fusions in acquired resistance (51). However, Vitale et al. (48) did not observe a clear association between ESR1-AKAP12 or ESR1-ARMT1 and ET-resistance, which may be due to the limited size of the ET-treated cohort. Importantly, they found neither fusion in normal breast tissues, ductal carcinoma in situ (DCIS), benign fibroadenomas, or metastatic tumors, highlighting their specificity to primary ET-treated tumors. Thus, the functional significance of ESR1-AKAP12 and ESR1-ARMT1 fusions in driving ET-resistance remains undefined.

In-frame ESR1-e6 fusions are rarely detected in primary tumors. In contrast, out-of-frame fusions with ESR1 gene breakpoints in exons 3–6 and in-frame fusions with ESR1 exon 7 have been reported more frequently in primary tumors; however, none have been shown to be pathogenic (52). ESR1-NOP2, the only in-frame ESR1-e6 fusion detected in primary tumors, while expressing a stable fusion protein, failed to confer ET resistance in functional studies (53). To date, no characterized ESR1 fusions that contain segments of ERα and are causative of ET resistance have been found in a primary tumor. These findings suggest that ESR1-e6 fusions function as drivers of ET-resistance later in tumor progression with emerging selection pressures from the use of ETs (Figure 2).

Figure 2 Distribution of ESR1 alterations across breast cancer progression. This figure summarizes the major classes of ESR1 alterations and their emergence across breast cancer stages. ESR1-CCDC170 is currently the only alteration reported in stage 0 DCIS and becomes enriched in primary invasive tumors. It is not known if ESR1-CCDC170 confers ET resistance at the DCIS stage (denoted as a “?” symbol). In primary tumors, the ESR1-CCDC170 fusion confers ET resistance (denoted as “+” symbol). ESR1-AKAP12 and ESR1-ARMT1 are recurrent fusions identified in primary tumors, but they do not confer ET resistance (denoted as “–” symbol). ESR1 LBD mutations (denoted with red asterisk) are significantly enriched in ET-treated, metastatic tumors, representing the most common mechanism of ET resistance. ESR1 exon 6 fusions are detected almost exclusively in metastatic disease after prolonged ET exposure, as drivers of ET resistance. The estimated prevalence for ESR1-e6 fusions comes from summary of all studies cited in this review. Key for references in the figure: a, (48); b, (29). This figure was created using BioGDP, developed by Jiang et al. (Nucleic Acids Res, 2025;53:D1670-6; doi: 10.1093/nar/gkae973). AF, activation function; DBD, DNA-binding domain; DCIS, ductal carcinoma in situ; ET, endocrine therapy; H, Hinge region; LBD, ligand-binding domain; WT, wild-type.

ESR1 fusions in metastatic tumors

To better understand the role of ESR1 fusions in late-stage ER⁺ breast cancer, Dr. Matthew Ellis’ laboratories discovered two in-frame inter-chromosomal translocation events involving ESR1 with YAP1 and PCDH11X (ESR1-e6>YAP1 and ESR1-e6>PCDH11X) from ET-refractory, metastatic ER⁺ patients (2/25 late-stage ER⁺ samples, 8%) (53,54). In contrast to ESR1-CCDC170 fusions, the ESR1-e6>YAP1 and ESR1-e6>PCDH11X fusion proteins retained the first six exons of ESR1 (ESR1-e6) encoding the AF1, DBD, and hinge region of ERα fused to C-terminal sequences of partner genes, thus losing the LBD. Both fusions were able to express stable ESR1 fusion proteins that drove expression of target genes in an E2-independent manner. Interestingly, they also induced strong expression of epithelial-to-mesenchymal transition (EMT) genes and promoted metastasis in experimental mouse models, a property that was not observed with liganded WT ERα (53). These data indicate that these ESR1 fusion proteins have unique pro-metastatic properties. However, the ESR1-e6>YAP1 and ESR1-e6>PCDH11X fusions were identified in a small cohort of late-stage ER⁺ samples and the landscape of pathogenic ESR1 fusions in late-stage ER⁺ breast cancer is still incomplete.

The clinical landscape, including a broader variety of ESR1 fusions, was further investigated by others. Hartmaier et al. (55) reported the discovery of recurrent ESR1 fusion events in metastatic, ER⁺ breast cancer that are associated with ET-resistance. They identified 88 structural rearrangements impacting the ESR1 gene across 83 patients and validated 9 fusion transcripts encoding ESR1 fusion proteins, all involving breakpoints in or near intron 6 and thus truncating the LBD. Among these fusions, three demonstrated ligand-independent, ET-resistant transcriptional activity in a luciferase reporter gene assay in transfected HEK293T cells. Robinson et al. (56) identified three additional ESR1-e6 fusions, ESR1-e6>DAB2, ESR1-e6>GYG1, and ESR1-e6>SOX9, in an integrative genomic analysis of patients with metastatic solid tumors. Another whole-genome analysis of metastatic solid tumors found seven additional ESR1-e6 fusions in ER⁺ MBC cases (57). However, none of these fusions were biologically characterized.

We therefore comprehensively screened all known 15 in-frame ESR1-e6 fusions with diverse partner genes identified from the above-mentioned independent cohorts (53,55-57). Remarkably, all follow a genomic format that preserves the first six exons of ESR1 fused in-frame to a C-terminal partner gene that replaces the ESR1 LBD (58). Among them, we identified 10 functionally active fusions that promoted E2-independent cell growth, motility, invasion, and resistance to the SERD fulvestrant (58). Active ESR1 fusion proteins are nuclear-localized, bind EREs within E2-regulated genes, and recruit transcriptional CoAs to initiate gene expression to drive their phenotype (53,58-60) (Figure 1C).

Immunofluorescence assays demonstrated that the inactive ESR1 fusion proteins retained the ability to enter the nucleus. Furthermore, ESR1 fusion proteins did not form heterodimers with WT ERα in co-immunoprecipitation assays. Together, these findings indicate that the inactive ESR1 fusion proteins do not function in a dominant-negative manner, which is consistent with the observation that cells expressing these fusions maintain normal growth in response to E2 (53,58).

RNA sequencing (RNA-seq) revealed an active ESR1 fusion-specific gene expression pattern that is enriched with estrogen-responsive and EMT genes (58). Unlike other gene fusions in cancers, ESR1 fusions are characterized by the extreme diversity of 3' partner genes. Their biological activity cannot be solely predicted by the functions of partner genes, thus creating a considerable diagnostic challenge. Fusion proteins involving a known TF or CoA gene, including ESR1-e6>YAP1, ESR1-e6>SOX9, ESR1-e6>ARNT2, ESR1-e6>LPP, and ESR1-e6>NCOA1 drove ET-resistant cell growth and motility. However, ESR1-e6>TCF12, a fusion with a TF partner, did not induce these properties. Four fusion proteins that contain protein-protein interaction domains without known transcriptional roles, ESR1-e6>PCDH11X, ESR1-e6>CLINT1, ESR1-e6>GRIP1 and ESR1-e6>TNRC6B, are highly active, which would not have been predicted. Interestingly, one fusion protein, ESR1-e6>DAB2, was active in MCF7 cells, but not T47D cells, highlighting that cell context matters for some fusions to be active (58).

Because ESR1 fusions are heterogeneous and not routinely screened for clinical diagnostics, we developed a diagnostic 24-gene expression signature for the presence of an active ESR1 fusion protein by assembling highly enriched genes expressed by active ESR1 fusions compared to inactive ones (58). This signature was further validated in 22 ERα⁺ patient-derived xenografts (PDXs). Importantly, the signature not only successfully detected a PDX naturally expressing the ESR1-e6>YAP1 fusion (WHIM18), but also accurately diagnosed the presence of activating ESR1 LBD mutations (Y537S/N and D538G). The signature distinguished ET-resistant tumors driven by mutant or translocated ERα proteins from WT PDXs, with an accuracy of 95.0% (specificity, 88.9%; sensitivity, 100%). Finally, the signature was confirmed in 55 ER⁺ MBC patients in the MET500 cohort (56), significantly distinguishing active ESR1 point mutations (Y537S, D538G, and Y537C) and the ESR1-ARNT2-exon18 fusion from WT ESR1, with a sensitivity of 92.9% and a specificity of 78.0%. These characteristics suggest that the signature represents a practical molecular assay to screen for functionally active ESR1 fusions in ER⁺ MBC, which are otherwise difficult to detect and interpret given their structural heterogeneity. This signature may help stratify patients whose tumors harbor ESR1 fusions that drive ET resistance. We therefore called the diagnostic signature MOTERA for “Mutant or Translocated ER Alpha” (58).

In concordance with our study, Yates et al. (59) showed that ESR1 fusions exhibited E2-independent activity not only T47D cells that represent an invasive ductal carcinoma (IDC) line, but also in an invasive lobular carcinoma (ILC) cell line, MDA-MB-134-VI. They also validated the enrichment of MOTERA signature genes in their T47D ESR1 fusion expressing models in an ET-resistant manner (59).

In addition to “canonical” genomic signaling, ESR1 fusion proteins may potentially act in a non-canonical genomic or non-genomic manner. They lack the LBD but retain the N-terminal AF1, DBD, and hinge region from WT ERα that allows ERα to bind (tether to) other TFs such as AP-1 and Sp1 (13,14). Furthermore, transcriptomic profiling of T47D cells expressing active ESR1 fusion proteins demonstrated overlapping enriched pathways, such as estrogen response and EMT, as well as unique variations between different fusion partners that might contribute to the varying levels of ET-resistance (58,59). ESR1 fusions involving CoA partners, like ESR1-e6>YAP1, may have activity via the transcriptional machinery recruited by the YAP1 protein C-terminus. Moreover, we found that ESR1 fusion proteins expressed in breast cancer cells led to increased expression of multiple RTK kinases, such as RET, IGF1R, FGFRs, and activated downstream ERK and AKT signaling pathways (61), which may, in turn, phosphorylate various TFs and CoAs.

Prevalence

ESR1 fusions have been identified in varying proportions across studies, with an overall occurrence ranging from 1% to 10% in ERα⁺ breast cancers. Brett et al. (50) reported ESR1 fusion frequencies ranging from 1–10% in ER⁺ breast cancers, including untreated and early-stage tumors. Similarly, Heeke et al. (47) identified ESR1 fusions in 1.6% of tumors from a combined cohort of primary and MBCs across all subtypes, with 93% of in-frame fusions involving a breakpoint at exon 6. In metastatic disease, ESR1 fusion frequencies remain underestimated when assessed across unselected or pan-subtype cohorts. Hartmaier et al. (55) estimated a prevalence of at least 1% in metastatic breast tumors across all subtypes, with frequencies estimated ten times higher from circulating tumor DNA (ctDNA). Priestley et al. (57) observed ESR1 fusions in 1.7% of MBCs (7 of 410 cases). Similarly, the Metastatic Breast Cancer Project (62) identified ESR1 fusions in approximately 1% of late-stage breast cancer patients (4 of 379 cases). More recently, Basu et al. (63) reported a higher frequency of ESR1 fusions in ER⁺/HER2⁻ breast cancer metastatic samples versus primary tumors (5.3% versus 2.0%, respectively).

Notably, higher frequencies of ESR1-e6 fusions have been reported in studies employing ET-treated, metastatic ER⁺ tumors, consistent with the role of ESR1-e6 fusions in endocrine resistance. Lei et al. (53) identified ESR1 fusion events in 8% of advanced, endocrine-resistant ER⁺ breast cancer samples (2 of 25 cases). Analysis of the MET500 dataset (56) revealed a prevalence of ~5%, with three ESR1-e6 fusions detected among 55 MBC cases (58). Furthermore, a presentation at the San Antonio Breast Cancer Symposium (SABCS) in 2023 reported that 13 of 14 identified ESR1 fusions were found in luminal B metastatic tumors, corresponding to a frequency of 6.5% (64). A more recent presentation at SABCS 2025 reported an ESR1 fusion frequency of 4–10% in metastatic ER⁺/HER2⁻ breast cancer patients heavily treated with ET (65). As ESR1 exon 6 fusions represent a distinct mechanism of resistance to therapies targeting ESR1 LBD missense mutations, expanding use of oral SERDs may exert selective pressure favoring the emergence of these fusions.

Together, these findings indicate that ESR1 exon 6 fusions are selectively enriched in ET-treated metastatic ER⁺ breast cancers (Figure 2), and that their true incidence is likely underestimated in unselected or pan-subtype cohorts. Accurate prevalence estimates require sensitive fusion-detection methods applied to appropriately selected patient populations. As RNA-seq becomes more widely integrated into clinical diagnostics and the use of next-generation oral SERDs increases, the frequency of ESR1-e6 fusion events in advanced breast cancer will be more accurately defined.

Formation of fusion genes

Despite the emerging studies that have detected ESR1 fusions in breast cancer, the detailed mechanisms by which ESR1 fusion events arise remain unaddressed. The formation of an oncogenic fusion gene has been shown due to double-stranded DNA breaks (DSBs) and dysregulated DSB DNA repair by the error-prone non-homologous end joining (NHEJ) pathway. E2-liganded ERα can form a complex with PARP-1, DNA topoisomerase TOP2B, and DNA-dependent protein kinase (DNA-PK) at EREs of its target genes in breast cancer cells (66). Recruitment of TOP2B induces DSBs (66,67), with DNA-PK present to trigger DSB repair (68). Under conditions of defective NHEJ, these breaks may give rise to chromosomal translocations in breast cancer cells (69). Inhibition of PARP-1 activity (70) and depletion of TOP2B (71) can decrease translocations in model systems, while DNA-PK inhibition can stimulate translocations (72). Whether PARP1 or TOP2B inhibitors can prevent ESR1 chromosomal translocations remains to be investigated.

The SERM tamoxifen was reported to induce DSBs in MCF7 breast cancer cells through generation of free radicals, although at high concentrations of 5–10 µM (73). A subsequent study that treated T47D breast cancer cells with 7.5 µM of either tamoxifen or the SERD fulvestrant for four hours showed that DNA damage was increased (as assayed by accumulation of the DSB marker, γH2AX) with either ET (74). The mechanism behind the increased DNA damage by the ETs was the downregulation of the ERα target gene phosphodiesterase 4D that resulted in increased cyclic AMP, PKA kinase activation, and generation of reactive oxygen species (74). Thus, we speculate that ET treatment may promote DNA damage at the ESR1 locus. Erroneous repair of these breaks via chromosomal translocations could result in the formation of diverse ESR1 fusions. Among these, expressed fusion proteins that retain the ability to activate ER proliferative signaling in an E2-independent manner would confer a selective advantage under ET, allowing these cells to expand as the dominant clone, while wild-type ERα-expressing cells would be suppressed (Figure 3).

Figure 3 Emergence and selection of ESR1 fusion-positive clones under ET pressure. The figure illustrates the selection of ESR1 fusion-expressing tumor cells during ET. In untreated tumors, E2-dependent signaling drives proliferation and tumor growth, and WT ESR1-expressing cells represent the dominant population. ET suppresses ER signaling, causing cell death and regression of WT ESR1 clones. ET may cause DSBs at the ESR1 locus. Repair through chromosomal rearrangement can generate in-frame ESR1 fusions. Cells expressing non-functional fusions are lost. Cells expressing ‘active’ ESR1 fusions are “selected” as these fusions support E2-independent growth. As such, these cells expand and dominate the tumor driving ET-resistant disease. This figure was created using BioGDP, developed by Jiang et al. (Nucleic Acids Res, 2025;53:D1670-6; doi: 10.1093/nar/gkae973). AI, aromatase inhibitor; Chr, chromosome; DSB, double-stranded DNA break; E2, estradiol; ER, estrogen receptor; ERE, estrogen response element; SERDs, selective estrogen receptor degraders; SERMs, selective estrogen receptor modulators; WT, wild-type.

Co-occurring mutations with ESR1-e6 fusions

As the emergence of ESR1-e6 fusions has only been recognized within the past decade, the broader mutational landscape accompanying these variants is poorly understood. It is now clear that ESR1 fusions can co-occur with the more prevalent ESR1 LBD point mutations. Upon analysis of 55 ER⁺ cases in the MET500 study (56), we previously identified two ESR1 fusions, but one of them (ESR1-ARID1B) was found co-expressed with the ESR1 LBD D538G mutation (58). Heeke et al. (47) found concurrent LBD point mutations in only 7 out 76 tumors harboring ESR1 fusions. Similarly, Brett et al. (50) reported a tumor from a single patient to have ESR1-PLEKHG1 and ESR1-CCDC170 fusions (both with ESR1 exon 6 breakpoints), alongside an ESR1 Y537N mutation. Hartmaier et al. (55) also identified ESR1 LBD mutations co-occurring with ESR1-e6 fusions and noted these to be the most common co-occurring alterations in ESR1 fusion-positive tumors. They speculate that the prevalence of such co-occurrences may increase with the expanded use of more targeted ET therapies against LBD mutants, with the creation of ESR1 fusions as a subsequent resistance mechanism. Two recent posters from the SABCS 2025 conference also reported ESR1 LBD point mutations co-occurrence with ESR1 fusions in ~60% of the ESR1 fusion cases identified (65,75). Further investigation is necessary to evaluate whether the co-occurrence of multiple ESR1 alterations contributes to enhanced ET resistance and more aggressive disease outcomes.

Interestingly, ESR1-e6 fusions are overwhelmingly identified in HER2-negative tumors, suggesting ESR1-e6 fusion-driven tumors do not rely on HER2 signaling. Supporting this, two reported cases describe patients whose primary HER2-positive tumor lacked detectable ESR1 fusions, which later emerged in the metastatic HER2-negative tumor (50,55). These data suggest that the presence of ESR1-e6 fusions may replace HER2 as a dominant oncogenic driver. Other recurrent alterations in ER+ tumors, such as activating mutations in the PI3K/AKT pathway and PTEN loss, in the mitogen-activated protein kinase (MAPK) signaling cascade (ERBB2/HER2, NF1 loss, and FGFR4), and TP53 mutations, are frequently implicated in ET resistance (76,77). Interestingly, ESR1 LBD point mutations and ERBB2/HER2 and NF1 alterations were mutually exclusive (65). However, the extent to which these alterations co-occur with ESR1-e6 fusions and contribute to the metastatic disease phenotype remains to be systematically evaluated.

Detection techniques and challenges

ESR1 fusions have been detected using multiple genomic and transcriptomic approaches across different studies. However, the heterogeneity and unknown identity of the 3’ partner gene complicates detection by traditional methods like fluorescent in situ hybridization (FISH) and polymerase chain reaction (PCR) techniques. While few ESR1 fusions have been detected by whole-exome sequencing (WES) (56,78), it can miss many genomic rearrangement events and remains suboptimal in this regard.

Whole-genome sequencing (WGS) has enabled the identification of numerous ESR1 fusions. For example, Hartmaier et al. (55) detected ESR1-e6>DAB2 and ESR1-e6>GYG1 in their metastatic patient samples, and Priestley et al. (57) identified seven distinct ESR1-e6 fusions in their metastatic samples. Despite these advances, high background noise challenges reliable fusion detection using WGS (78).

RNA-seq has proven effective in identifying ESR1 fusions, including the well-characterized ESR1-CCDC170 and ESR1-e6>YAP1 fusions (46,54). Lei et al. (53) used RNA-seq to uncover multiple ESR1 fusions with different exon breakpoints in both primary and metastatic tumors. However, RNA-seq-based fusion calling can yield false positives. Giltnane et al. (51) predicted 346 fusion events across 50 samples, requiring quantitative PCR (qPCR) and Sanger sequencing for validation—ultimately, only confirming 26 events, including ESR1-ARMT1 and ESR1-AKAP12 fusions. Furthermore, the clinical implementation of RNA-seq for diagnosis of ESR1 fusions remains limited by requirements for high-quality RNA, sufficient sequencing depth and coverage of fusion junctions. To overcome these technical obstacles, Matissek et al. (78) developed anchored multiplex PCR, a targeted and clinically applicable approach for identifying gene fusion events. This method was later adopted by Brett et al. (50) to identify ESR1 fusions in patient metastatic tumor samples.

While most ESR1 fusions were identified in solid breast tumors, three ESR1 fusions (two exon 6, one exon 7) were detected in ctDNA (55). ctDNA may serve as a minimally invasive approach for fusion detection. However, further studies are required to validate and compare the sensitivity of fusion detection in ctDNA versus solid tumor samples. While several sequencing-based approaches have enabled ESR1 fusion detection, a standardized and clinically feasible detection system remains to be developed. The range of detection techniques used across different studies to identify specific ESR1 fusions has been thoroughly described previously (79).

Poor patient outcomes when expressing ESR1 fusions

Do patients with metastatic lesions expressing an ESR1 fusion have worse clinical outcomes than those that do not? In the literature, only individual patients with an ESR1 fusion have been documented to be ET-resistant (51,54,55). This important clinical question needs extensive real-world sequencing and outcome data. Two recent posters from the SABCS 2025 conference begin to address this issue. Researchers from Guardant Health reported that known and “likely” active ESR1-e6 fusions were associated with an increased risk of early death, as compared to “no fusion” cases, unless a CDK4/6 inhibitor (CDK4/6i) was used in combination with an AI (75). Researchers from the Dana Farber Cancer Institute reported that patients with ESR1 fusions had poor clinical outcomes, such as limited time on treatment (ToT) for both combination ET and oral SERDs (65).

Mechanisms that active ESR1 fusions utilize inform therapeutic opportunities

Limitations of current therapies

All current ETs disrupt E2-ERα signaling to suppress ERα-driven transcription. While AIs reduce E2 production, all other ET classes directly target the LBD of ERα. ESR1 LBD mutant proteins can be inhibited by new oral SERDs [elacestrant (32) and imlunestrant (80)] that are now FDA-approved. As ESR1-e6 fusion proteins lack the LBD and function independently of E2, they confer pan-ET resistance.

Following progression on ET, patients are often treated with ET in combination with targeted agents when actionable co-occurring alterations are identified. However, the limited understanding of recurrent driver mutations co-occurring with ESR1-e6 fusions leaves the therapeutic relevance of such targeted agents somewhat unclear. As highlighted above, ESR1 LBD point mutations do co-occur with ESR1 fusions, which suggests that new oral SERD treatment should be given to inhibit the ESR1 LBD point mutant and a CDK4/6i to inhibit the ESR1 fusion. Activation of the PI3K pathway is a common secondary mechanism of ET resistance that can be targeted by combining ET with an α-specific PI3K inhibitor (alpelisib) or a pan-AKT inhibitor (capivasertib) (81). To date, only two cases of co-occurring ESR1 fusions with an activating PIK3CA have been reported, and the sensitivity of ESR1 fusion-driven tumors to PI3K inhibition has not been systematically evaluated (50,54). Likewise, although active ESR1-e6 fusion proteins upregulate the mTOR signaling axis (59), the therapeutic impact of targeting this pathway is currently unexplored. PARP inhibitors, approved for metastatic ER⁺/HER2⁻ breast cancers with germline BRCA1/2 mutations, have been given to patients who progressed on ET and CDK4/6i (82). Utility of PARP inhibitors for treatment of ESR1 fusion-positive tumors has not been tested but would likely be restricted to rare cases with coincident BRCA1/2 alterations.

The above knowledge gaps highlight the need for real-world analysis of ESR1 fusions to identify recurrent actionable co-occurring alterations and identify targetable pathways uniformly activated by these fusions. The current limited landscape of actionable co-alterations restricts the use of approved targeted agents, arguing for alternative strategies. Our finding that active ESR1 fusions with diverse 3' partners converge on common transcriptional (58) and kinome (61) reprogramming supports the existence of shared downstream dependencies. Targeting these common networks, rather than individual fusions or sporadic co-mutations, may represent a more effective and generalizable therapeutic strategy.

Coactivator inhibition

The underlying mechanism(s) of how ESR1 fusion proteins promote transcriptional activity remain unknown. Our prior study indicated that the 26S proteasome was enriched in ESR1-e6>YAP1 fusion protein transcriptional complexes compared to WT ERα and the ERα-Y537S point mutant using an ERE DNA pulldown assay (60). Inhibition of the proteasome blocked ESR1-e6>YAP1 fusion-driven transcriptional activation. The growth of T47D ESR1-e6>YAP1 fusion expressing cells was suppressed by bortezomib (60), a proteasome inhibitor FDA-approved for use in multiple myeloma. Interestingly, a Phase II trial showed that combinatorial use of bortezomib with fulvestrant enhanced progression-free survival of AI-resistant patients at 12 months (83). However, since the components to form transcriptional complexes were provided by nuclear extracts from HeLa cervical carcinoma cells rather than ER+ breast cancer cells, similar proteomic studies are required using ER+ breast cancer cells to extend these findings.

Kinase inhibition

Lei et al. (53) demonstrated that breast cancer cell/tumor growth driven by ESR1-e6>YAP1 or ESR1-e6>PCDH11X proteins remained sensitive to the CDK4/6i palbociclib both in vitro and in vivo in a PDX (called WHIM18) naturally expressing the YAP1 fusion, with significant suppression of tumor growth at primary and metastatic sites. Thus, CDK4/6 inhibition may be a therapeutic vulnerability in ER+ breast cancers expressing active ESR1-e6 fusion proteins and suggests that detection of such fusions could help stratify patients for CDK4/6i-based therapy. Notably, the therapeutic benefit of palbociclib has been observed clinically—two ER⁺ MBC patients harboring ESR1-e6 fusions benefited from different CDK4/6i (50). However, CDK4/6i exerts a cytostatic effect on ESR1 fusion-positive tumors, raising the question of which additional agent should be combined with a CDK4/6i to achieve complete tumor regression (Figure 1).

To further explore additional targetable vulnerabilities, we extended this work to a kinome-wide analysis of ESR1 fusion-driven breast cancer (61). Proteomic profiling using kinase inhibitor pulldown assays revealed that active ESR1 fusions upregulate the levels of multiple kinases, including REarranged during Transfection (RET), IGF1R, FGFRs, and JAK1. These alterations create a new therapeutic vulnerability despite the tumors being unresponsive to conventional ET-based treatments. We further demonstrated that RET inhibition using an FDA-approved drug (pralsetinib) significantly suppressed the growth of ESR1 fusion-driven breast cancer models, both in cell lines and in PDXs (61). Furthermore, combining RET inhibition with palbociclib reduced growth of ER⁺ breast cancer cell lines expressing active ESR1-e6 fusions. These findings suggest that RET acts as a key survival pathway in ESR1 fusion-driven cancers and that RET inhibitors, alone or in combination with existing therapies, may represent a promising treatment strategy for ESR1-translocated breast cancer patients (61,84).

Translational inhibition

Canonical eukaryotic protein synthesis is dependent on the eukaryotic initiation factor 4E (eIF4E), which binds the 5'-7-methylguanosine cap of mRNA, initiating the process of “cap-dependent” translation. In contrast, certain transcripts utilize a “cap-independent” translational mechanism that relies on complex secondary structures in the 5'-untranslated region (UTR) of their mRNAs. This mechanism is dependent on the RNA helicase, eIF4A, which unwinds RNA hairpin structures to help initiate translation. Boyer et al. (85) recently demonstrated that ESR1 mRNA is translated via the cap-independent mechanism. eIF4A inhibition decreased ERα-mediated translation and breast cancer cell proliferation. Interestingly, the growth of T47D cells driven by a CRISPR/Cas9-engineered ESR1-e6>SOX9 fusion was inhibited by an eIF4A inhibitor (silvestrol), suggesting ESR1-fusion driven tumors may be likewise dependent on eIF4A for their translation. Currently, the eIF4A inhibitor zotatifin is in a Phase 1–2 clinical trial for ER⁺ MBC patients, either in combination with fulvestrant, or with fulvestrant and the CDK4/6i abemaciclib (Clinical Trials.gov ID: NCT04092673). The work of Boyer et al. (85) opens a new area of investigation into translational control as a potential therapeutic vulnerability of ESR1-fusion driven tumors.

Immunotherapies

In contrast to other solid tumors, immunotherapy is understudied in ER⁺ breast cancer due to the predominance of immunogenically “cold” tumors without tumor-infiltrating lymphocytes. Estrogen signaling contributes to this phenotype by promoting an immunosuppressive tumor microenvironment (TME) (86) (Figure 4A). Accordingly, ETs can increase immune infiltration of anti-tumor immune cell populations and enhance immunogenicity (Figure 4B) (88). ER⁺ breast tumors expressing pathogenic ESR1-e6 fusions, such as ESR1-E6>YAP1, are likely to be poorly immunogenic due to the following in silico analyses: (I) tumors harboring gene fusions tend to have lower burden of mutations in these genes than those with mutations only, which has been found in a panel of oncogenic genes, including ESR1, in many cancer types (89). Low mutational loads in ESR1-translocated breast tumors likely will produce few neoantigens. (II) In-frame fusions produce low levels of neoantigenic epitopes compared to frameshift fusions (89), since in-frame fusions preserve the same peptides as in fusion partner proteins. Since ESR1 fusions are an underappreciated mechanism of somatic mutations that drive tumor growth and metastasis, whether and how expression of an ESR1 fusion protein may modulate the TME is currently not known (Figure 4C). Defining the TME that emerges in heavily ET-treated tumors harboring ESR1 fusions will be important for identifying potential therapeutic vulnerabilities and determining whether immunotherapy may provide clinical benefit in this subset of ER⁺ MBC.

Figure 4 Tumor microenvironment remodeling under ET therapy and ET resistance. In treatment-naïve ER⁺ breast tumors, E2-ERα signaling maintains an immunosuppressive TME characterized by low cytotoxic immune infiltration and enrichment of pro-tumor immune cell populations and certain chemokines [e.g., CCL2, CCL5 (87)]. Endocrine therapies (SERMs/SERDs/AIs) increase immune infiltration and generate a more inflammatory TME. The immune landscape that emerges after ET resistance driven by an ESR1 fusion protein-expressing tumor is currently undefined. Determining how ESR1 fusion proteins reshape tumor-immune interactions may uncover new exploitable therapeutic vulnerabilities. This figure was created using BioGDP, developed by Jiang et al. (Nucleic Acids Res, 2025;53:D1670-6; doi: 10.1093/nar/gkae973). AI, aromatase inhibitor; E2, estradiol; ERα, estrogen receptor-alpha; ET, endocrine therapy; IFN, interferon; SERDs, selective estrogen receptor degraders; SERMs, selective estrogen receptor modulators; TME, tumor microenvironment; WT, wild-type.

As ESR1 fusion-driven tumor growth can be suppressed by a CDK4/6i, the immunoregulatory effects of these agents on ER⁺ tumors are particularly relevant. Both palbociclib and abemaciclib have been shown to enhance the immunogenicity of ER⁺ tumors and promote a “hotter” immune signature (88). A transcriptomic study additionally revealed an enrichment of anti-tumor immunity profile in biopsies from ER⁺ patients treated with palbociclib (90). Abemaciclib enhanced tumor immunogenicity by elevating antigen presentation and suppressing regulatory T cell (Treg) proliferation in a HER2-positive transgenic mouse model (90). Importantly, CDK4/6 inhibition selectively suppressed Treg cells rather than cytotoxic T cells and helper T cells likely due to higher expression of the CDK4/6i target retinoblastoma protein (Rb) in Treg cells (90). Clinical trials exploring the use of different CDK4/6i and immune checkpoint inhibitors for efficacy in ER⁺ MBC patients are ongoing [reviewed in (88)]. Further research is needed to address how to strengthen the immunogenicity of breast tumors harboring driver ESR1 fusions and leverage their potential immunotherapeutic vulnerabilities.

Experimental models

To study expressed ESR1 fusions, we and others have used a range of experimental models including: (I) luciferase reporter assays in transfected HeLa, HEK 293T, or breast cancer cells (53,55,59,60) to assay ERE-driven transcriptional activity; (II) we have used ER⁺ breast cancer cell lines (e.g., MCF7, T47D), where ESR1 fusion cDNA constructs were stably expressed by lentiviral transduction to assess E2-independent growth, motility, drug resistance and transcriptomic reprogramming (58,60,61); (III) similar lentiviral-based ER⁺ cell line models (T47D, MDA-MB-134-VI) were employed by Yates et al. (59) in their ESR1 fusion functional studies, but after prior knockdown of WT ESR1; (IV) ER⁺ PDXs, especially WHIM18 that naturally expresses the ESR1-e6>YAP1 fusion (54), have been used to study in vivo tumor growth and therapeutic drug response (53,61); and (V) ER⁺ PDX-derived organoids (PDxOs), which allow ex vivo testing of drug sensitivity and molecular profiling in a 3D culture system that more closely mimics a patient’s tumor (61). These model systems have been critical for identifying functional ESR1 fusion proteins, their transcriptionally directed programs, and potential vulnerabilities to treatments (e.g., CDK4/6i or RET inhibitors).

To more accurately reproduce tumor-related ESR1 translocation events, endogenous knock-in of the fusion sequences with CRISPR/Cas9 technology will be an important modeling for the future. CRISPR/Cas9 technology has generated recurrent fusions identified in leukemia and sarcoma patients in human cancer cell lines (91) and also a ESR1-e6-SOX9 fusion was successfully engineered in T47D cells (85). Importantly, this method will facilitate studies on chromosomal rearrangements involving the ESR1 gene that may interrupt the function of tumor suppressor partner genes, thereby leading to malignancy, regardless of the fusions being in-frame or out-of-frame.

Conclusions

Since the discovery in 2013 of the first in-frame ESR1-e6 fusion (expressing the ESR1-e6->YAP1 protein) in an ER+ metastatic sample that was subsequently propagated as a PDX (WHIM18) (54), there have been additional clinical reports of different ESR1-e6 fusions. However, there are still major unaddressed questions to be resolved by future research, as discussed below.

What is the prevalence of ESR1-e6 fusions capable of producing in-frame chimeric proteins?

As cited above, all types of ESR1 fusions have been estimated from 1–10%. However, these publications employed small, mixed cohorts spanning multiple breast cancer subtypes, stages, and treatment regimes. Accurate estimation of ESR1 fusion prevalence will require analysis of real-world clinical sequencing data from appropriately defined ER⁺ MBC cohorts receiving ET. Also, with the advent of new oral SERDs to treat ESR1 LBD mutated metastatic tumors, we predict that the number of ESR1-e6 fusions may increase as a resistance mechanism to remove the mutant LBD from ERα.

When should an oncologist test for an ESR1-e6 fusion?

As drivers of ET resistance, ESR1-e6 fusions have been exclusively observed in patients with ER⁺ MBC and prior ET exposure. Testing for ESR1 fusions should therefore be considered in patients with advanced disease who are progressing on ET (especially after the use of SERDs), particularly when standard ctDNA assays do not identify ESR1 LBD mutations or other known drivers of ET resistance. In such settings, unexplained ET resistance warrants evaluation for the presence of an ESR1-e6 fusion. Due to the heterogeneity of the 3’ partner, ESR1 fusions can only be identified by unbiased genomic screening techniques, which are not routinely implemented in clinics. Moreover, genomic identification alone cannot distinguish an ‘active’ driver ESR1 fusion from an inactive passenger, complicating the clinical identification and interpretation of ESR1 fusions.

How can an oncologist determine if an ESR1-e6 fusion reported in an RNA-seq report is pathogenic or not?

There may be a simple idea that all ESR1-e6 fusions are drivers of ET-resistance, but from our previous studies, this is simply not the case (58,61). Thus, a diagnostic tool is sorely needed for the clinic to distinguish an active versus inactive ESR1 fusion in the patient biopsy. As cited above, we have developed a 24-gene set expression signature called “MOTERA” that active fusions express at a higher level than inactive ones (58). However, this signature needs validation from analysis of real-world data from clinical RNA-seq. Upon successful validation, this would allow the oncologist to know what therapy is needed. For example, an inactive ESR1-e6 fusion would not be the driver of tumor growth, unless ESR1 LBD mutations were detected, and the tumor would be driven by WT ERα. In this case, standard ET drugs would be appropriate. However, in the case of an active ESR1-e6 fusion, ET drugs will fail and treatment with a CDK4/6i should be continued as cited above.

What is/are the mechanism(s) that ESR1-e6 fusions employ to stimulate ET-resistant growth?

This is a key basic science question, as we and others have only published data revealing that studied ESR1-e6 fusion proteins, such as ESR1-e6>YAP1, ESR1-e6>PCDH11X, ESR1-e6>SOX9, stimulate transcription of ERE-containing luciferase reporter genes and endogenous ERα and EMT-related genes and bind to ERE sequences in the chromatin of ER+ breast cancer cell lines (53,55,58,59). This mechanistic class (Figure 5, schema ①) acts via “genomic signaling”, which has been well-characterized for E2-liganded WT ERα. As E2-liganded WT ERα can also promote cell proliferation via “tethering” to target genes via binding to other TFs, such as AP-1 and Sp1 (13,14), it will be important to determine if any ESR1-e6 fusion proteins may regulate AP-1/Sp1 target gene transcription (Figure 5, schema ②). Finally, E2-liganded WT ERα can stimulate certain downstream kinase pathways in a rapid, “non-genomic signaling” manner. While no current data exists for an ESR1-e6 fusion protein having this ability (Figure 5, schema ③), it remains a formal possibility for a fusion that drives ET-resistant growth but does not promote a high MOTERA expression score.

Figure 5 Genomic and potential non-genomic signaling mechanisms that ESR1 fusions may utilize to drive tumor growth and ET resistance. ESR1 fusion proteins may drive tumor growth and ET-resistance through distinct mechanisms. Schema ①, classical genomic signaling: ESR1 fusions bind EREs in target gene regulatory regions and recruit CoAs to activate target gene transcription. Schema ②, tethering to TFs: ESR1 fusions may bind DNA indirectly through tethering to TFs like AP-1/SP-1 bound to their respective DNA binding sites. Schema ③, non-genomic signaling: a membrane-bound ESR1 fusion may activate cytoplasmic kinase cascades that then drive proliferation and activate TFs/CoAs to modulate gene expression. Direct experimental evidence for the latter two mechanisms remains to be established. This figure was created using BioGDP, developed by Jiang et al. (Nucleic Acids Res, 2025;53:D1670-6; doi: 10.1093/nar/gkae973). AP-1, activator protein 1; CoA, coactivator; EMT, epithelial-to-mesenchymal transition; ERE, estrogen response elements; ET, endocrine therapy; SP-1, specificity protein 1; TFs, transcription factors.

Once an ER+ MBC patient has been diagnosed with an active ESR1-e6 fusion, what therapeutic approach is needed for full tumor eradication?

As cited above, a CDK4/6i can slow the growth of a PDX tumor driven by expression of an ESR1-e6 fusion (53). However, the tumor is still alive. Future research efforts will need to identify what other targeted therapy should be combined with a CDK4/6i to fully eradicate such tumors.

Acknowledgments

None.

Footnote

Peer Review File: Available at https://tbcr.amegroups.com/article/view/10.21037/tbcr-2025-1-63/prf

Funding: This study was funded by the DOD Breast Cancer Research Program Grant (No. W81XWH-21–1-0119, to C.E.F.) and the Adrienne Helis Malvin Medical Research Foundation through direct engagement with the continuous active conduct of medical research in conjunction with Baylor College of Medicine (No. M-2020, to C.E.F.).

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tbcr.amegroups.com/article/view/10.21037/tbcr-2025-1-63/coif). X.G. reports a patent on the above cited MOTERA gene signature (PCT/US2022/077924). C.E.F. reports grants from the DOD Breast Cancer Research Program Grant (No. W81XWH-21–1-0119) and the Adrienne Helis Malvin Medical Research Foundation (No. M-2020); a patent on the above cited MOTERA gene signature (PCT/US2022/077924); an unpaid editorial board role with the journal Steroids; and equity and salary support from CoRegen, Inc. The other author has no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.

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