Endocrine therapy remains the cornerstone of treatment for estrogen receptor-positive (ER+) breast cancer. By suppressing or antagonizing ER signaling, hormonal endocrine therapy offers an effective and less toxic systemic approach for breast cancer patients. However, resistance to hormonal therapy is common, and metastatic ER+ breast cancer continues to cause high cancer-related mortality rates globally [1, 2]. For decades, endocrine resistance was believed to be mainly due to loss of ER expression, pathway bypass mechanisms, or nonspecific cellular adaptation. This paradigm shifted fundamentally with the application of next-generation sequencing (NGS) to metastatic tumor specimens.

Multiple independent genomic analyses identified recurrent, activating mutations in the ESR1 gene encoding ERα, in patients with endocrine-resistant metastatic disease [1, 3]. These alterations were rare in treatment-naïve primary tumors but became enriched following aromatase inhibitor (AI) exposure, establishing a clear role for therapeutic selection pressure [1, 2]. ESR1 ligand-binding domain (LBD) mutations stabilize the receptor in a constitutively active conformation, enabling ligand-independent transcriptional signaling even in the absence of estrogen [1, 3]. This mechanism explains why continued estrogen deprivation becomes ineffective once these mutant clones emerge. Importantly, these tumors often retain partial sensitivity to agents that directly antagonize or degrade the receptor, providing a rational therapeutic target [4].

Another paradigm shift followed with the recognition that ESR1 mutations are readily detectable in circulating tumor DNA (ctDNA). Metastatic ER+ breast cancer frequently involves bone and visceral sites, where tissue sampling can be either challenging or technically compromised by decalcification. ctDNA offered an alternative, blood-based detection that captures tumor heterogeneity across multiple metastatic sites and permits serial monitoring over time [5–7]. ctDNA analysis provided more than a surrogate for tissue testing. Serial monitoring revealed that ESR1 mutations often emerge months before radiographic progression, with mutant allele fractions rising under continued AI therapy and declining when selective pressure changes [8–12]. These observations reframed resistance as a measurable, dynamic evolutionary process rather than a binary event.

The field then reached a critical milestone: therapeutic intervention based on ctDNA detection. The phase III PADA-1 (palbociclib and circulating tumour DNA for ESR1 mutation detection) trial demonstrated that detecting a rising ESR1 mutation in plasma could trigger an early endocrine switch that improved progression-free survival (PFS), even while maintaining cyclin-dependent kinase 4 and 6 (CDK4/6) inhibition [13–15]. Subsequent studies using next-generation oral selective ER degraders (SERDs) have strengthened the concept of molecularly guided interception rather than delayed salvage therapy [16, 17]. Concurrently, drug development has accelerated. Elacestrant became the first oral SERD approved specifically for ESR1-mutant metastatic breast cancer, supported by randomized data and regulatory analyses explicitly linking benefit to mutation status [17–23]. Additional agents (including camizestrant, imlunestrant, and proteolysis-targeting chimera (PROTAC)-based ER degraders such as vepdegestrant) have expanded the therapeutic armamentarium and raised new questions regarding optimal sequencing, combination strategies, and timing of intervention [16, 24–27].

Together, these advances positioned ESR1 mutations at the convergence of molecular genetics, liquid biopsy technology, and clinical decision-making [28]. They provided a model for how resistance mechanisms can be detected early, monitored longitudinally, and targeted in ways that alter clinical outcomes. This review examines the biology underlying the clinical relevance of ESR1 mutations, the evidence supporting ctDNA-based detection and intervention, and the practical considerations required to integrate ESR1 genotyping into routine clinical practice. Emerging directions are also explored, including artificial intelligence-assisted interpretation of ctDNA kinetics and adaptive trial designs that treat clonal evolution as a therapeutic target (Figure 1). These advances must be considered within the broader context of morphological, radiological, and molecular subtyping challenges in breast oncology.

In ER+ breast cancer, prolonged exposure to endocrine therapy selects for mutations in the ESR1 gene, which encodes ERα. These mutations account for a substantial proportion of endocrine resistance, ranging from approximately 36% in earlier reports [3] to 63.2% in more recent cohorts [1, 3, 17, 29]. These mutations predominantly occur in the LBD of ERα and result in ligand-independent receptor activation. This allows tumor proliferation despite estrogen deprivation therapies.

While ESR1 mutations are rare in untreated primary breast cancer, multiple studies have shown that these mutations become frequent in metastatic disease following exposure to AIs and other endocrine therapies. This pattern suggests that these mutations function as resistance mechanisms rather than primary oncogenic drivers. Among these mutations, Y537S and D538G are the most common, accounting for the majority of ESR1-mutant breast cancers [1, 3, 30, 31]. Individual studies report Y537S in 42.3% of cases and D538G in 38.5% of cases [30]. Similarly, Westenend et al. [32] identified D538G in 9 of 18 cases (50%) and Y537S in 7 of 18 cases (39%) in a metastatic cohort. The frequency of these mutations after aromatase therapy further reinforces their role in endocrine resistance. Other substitutions at codon 537, including Y537N and Y537C, were also detected at lower frequencies [30]. For instance, in one metastatic cohort, Y537N accounted for approximately 9% of ESR1-mutant cases and Y537C for approximately 4.5% [17]. Although these mutations are less common than Y537S, they still retain their activating properties and contribute to disease progression.

Moreover, mutations affecting codon 536 are reported less frequently but follow the same resistance mechanism. Westenend et al. [32] identified the L536H mutation in 2 of 18 ESR1-mutant metastatic tumors, while Venetis et al. [17] detected only a single codon 536 variant in their cohort, supporting the low prevalence of these alterations. Lastly, E380Q represents a rare ESR1 mutation with a distinct functional profile. This mutation occurs outside the helix 11-12 hotspot region and represents approximately 1.1–10% of ESR1 mutations depending on the cohort [31, 33–35]. E380Q enhances estrogen sensitivity rather than causes complete ligand-independent receptor activation. Nonetheless, this mutation is detected at lower frequencies across different cancer cohorts, underscoring that not all variants confer resistance through identical mechanisms [1, 31].

Polyclonal mutations are common and clinically significant (Table 1). Multiple ESR1 mutations are detected in 26–36% of ESR1-mutant cases, reflecting parallel evolutionary paths across metastatic sites [17, 36, 37]. This polyclonality has important therapeutic implications, as different ESR1 variants may respond differently to specific SERDs and other ER-targeting agents [38]. The presence of multiple mutations may necessitate combination therapy approaches rather than single-agent strategies. However, it should be noted that the apparent association between polyclonality and worse outcomes may be confounded by overall ctDNA burden (total mutant allele fraction), as polyclonal ESR1 mutations are more frequently observed in patients with high ctDNA load, which is itself a strong prognostic factor. After correcting for total ESR1-mutant allele frequency (MAF), polyclonality may play a limited independent prognostic role. Indeed, it is plausible that virtually all ESR1-mutant cases are polyclonal at a biological level, with minor subclones falling below the detection threshold of current assays.

Clinically, ESR1 mutations confer resistance to standard hormone therapies such as AIs by promoting ligand-independent activation of the ERs. As a result, tumors with these mutations can grow and progress despite estrogen-lowering strategies [1, 3]. In a genome engineering study, the Y537S mutation demonstrated the highest level of ligand-independent ER activity and required the highest drug concentrations to suppress ER signaling. This suggests that this mutation is frequently associated with greater resistance to anti-estrogen therapies, including Fulvestrant [38]. Mechanically, Y537S stabilizes helix 12 of the ER in its active conformation, making it harder for hormone therapies to turn the receptor off [3]. On the other hand, D538G retains somewhat greater responsiveness to ER degradation compared to Y537S, and treatments such as Fulvestrant remain more effective [38]. Beyond endocrine resistance, ESR1 mutations have been shown to modulate metastatic behavior, indicating a role in disease progression beyond therapy resistance alone [44]. It is important to note that ESR1 mutant tumors retain ER expression. As a result, these tumors remain hormonally driven, and endocrine therapy remains a viable treatment strategy. In contrast, tumors with loss of ER expression are associated with a significantly worse prognosis as endocrine therapies are no longer effective [30, 32].

The emergence of oral SERDs has transformed ESR1-mutant breast cancer from a biomarker-defined subgroup into a therapeutically actionable population. Meta-analyses demonstrate that oral SERDs improve PFS specifically in ESR1-mutant disease (HR 0.56, 95% CI 0.44–0.71), with no significant benefit in ESR1 wild-type tumors (HR 0.94, 95% CI 0.78–1.14), establishing mutation status as a predictive rather than merely prognostic marker [65, 66] (Table 2).

Elacestrant became the first U.S. Food and Drug Administration (FDA)-approved oral SERD specifically indicated for ESR1-mutant ER+/HER2– advanced breast cancer following the EMERALD trial, which demonstrated median PFS of 3.8 vs. 1.9 months compared with standard endocrine therapy (HR 0.55, 95% CI 0.39–0.77; P = 0.0005) [19, 22]. Notably, benefit was most pronounced in patients with ≥ 12 months prior CDK4/6i exposure, where median PFS reached 8.6 vs. 1.9 months (HR 0.41) [18]. Real-world data confirm these findings, with a median time-to-next-treatment of 7.9 months across 306 patients [66]. However, the OS endpoint was not met in EMERALD; the FDA approval summary reported an OS HR of 0.90 (95% CI 0.63–1.30) in the ESR1-mutant subgroup, with no statistically significant OS benefit [22].

Inluriyo (imlunestrant) received FDA approval in September 2025 based on EMBER-3, demonstrating a median PFS of 5.5 vs. 3.8 months in ESR1-mutant patients (P < 0.001) [25, 67]. Updated analyses show median overall survival (mOS) of 34.5 vs. 23.1 months (HR 0.60, 95% CI 0.43–0.86), though the prespecified significance boundary was not crossed [67]. The combination of imlunestrant with abemaciclib significantly improved PFS regardless of ESR1 status (median 10.9 vs. 5.5 months; HR 0.59) [25, 67]. It should be noted that the FDA approval of Inluriyo (imlunestrant) was for monotherapy in ESR1-mutant disease; the combination of imlunestrant with abemaciclib did not receive FDA approval.

Co-occurring alterations influence treatment sequencing. Approximately 10–15% of patients harbor concurrent ESR1 and PIK3CA mutations [69]. For patients with dual ESR1 and PI3K-pathway alterations, real-world data suggest elacestrant monotherapy achieves a median time-to-next-treatment of 5.2–6.3 months, comparable to outcomes in phase 3 studies [66, 69]. The National Comprehensive Cancer Network (NCCN) guidelines recommend capivasertib plus fulvestrant for patients with PIK3CA, AKT1, or PTEN alterations after CDK4/6i progression, while elacestrant or imlunestrant are options for ESR1-mutant disease [62]. The optimal sequencing of these targeted approaches remains an active area of investigation [70, 71]. Mechanistically, ESR1-mutant tumors may upregulate PI3K/AKT signaling as a compensatory survival pathway, creating a molecular rationale for combination targeting. However, the choice between a SERD-based approach (for ESR1-mutant disease) and a PI3K/AKT pathway inhibitor-based approach (e.g., capivasertib + fulvestrant for PIK3CA/AKT1/PTEN-altered tumors) in the second-line setting after CDK4/6i progression is currently mutually exclusive in clinical practice [72]. Given that endocrine therapy-based third lines remain rare, patients are unlikely to receive both agents sequentially, making the initial therapeutic decision after CDK4/6i progression a critical and potentially irreversible choice. Prospective head-to-head data comparing SERD-first vs. PI3K inhibitor-first sequencing in dual-mutant disease are lacking and represent a key unmet research need.

ESR1 mutations represent a paradigm-defining example of how molecular oncology can transform clinical practice—from mechanistic discovery through biomarker-guided intervention to regulatory approval of mutation-specific therapeutics. These LBD alterations, rare in treatment-naïve tumors but emerging in 20–40% of patients following AI exposure, drive constitutive ER activation that renders continued estrogen deprivation ineffective while preserving sensitivity to receptor degradation strategies. The convergence of ctDNA technology with serial monitoring has reframed endocrine resistance as a dynamic, measurable evolutionary process rather than a binary clinical event, enabling detection of ESR1-mutant clones months before radiographic progression. Randomized evidence from PADA-1 and SERENA-6 demonstrates that therapeutic intervention triggered by molecular emergence (rather than delayed until clinical progression) significantly improves PFS, establishing ctDNA-guided switching as a clinically validated strategy. The regulatory approval of elacestrant specifically for ESR1-mutant disease, followed by imlunestrant, marks a transition from empirical endocrine sequencing to genotype-directed therapy selection. As oral SERDs, PROTAC-based degraders, and combination strategies continue to mature, the remaining challenges are operational rather than conceptual: standardizing thresholds for “rising” mutations, integrating polyclonality into treatment algorithms, and optimizing sequencing with PI3K/AKT pathway inhibitors in patients harboring concurrent alterations. The ESR1 story thus provides a template for precision oncology in solid tumors, demonstrating that when mechanism, measurement, and therapeutic targeting align, resistance can be intercepted rather than merely observed. However, several important limitations should be acknowledged. OS data from the interception trials (PADA-1, SERENA-6) remain immature, and the EMERALD trial did not demonstrate a statistically significant OS benefit for elacestrant. The cost and infrastructure requirements of serial ctDNA monitoring present substantial barriers to global implementation, particularly in resource-limited settings. Furthermore, the mutually exclusive nature of current second-line therapeutic options (SERD vs. PI3K pathway inhibitor) in patients with dual alterations highlights a critical gap in evidence-based sequencing strategies. These operational and clinical challenges must be addressed to fully realize the promise of ESR1-guided precision oncology.