ESR1 testing on FFPE samples from metastatic lesions in HR+, HER2– breast cancer after progression on CDK4/6 inhibitor therapy
Venetis K, Cursano G, Scafetta R, et al. Breast Cancer Res. 2025;27(1):79.
Summary. This study investigated estrogen receptor 1 (ESR1) mutations in patients with hormone receptor–positive (HR+), human epidermal growth factor 2–negative (HER2–) metastatic breast cancer who progressed on endocrine therapy and cyclin-dependent kinase 4/6 (CDK4/6) inhibitor treatment. Next-generation sequencing (NGS) was performed on formalin-fixed paraffin-embedded (FFPE) tissue samples from metastatic sites in 38 patients. ESR1 mutations were detected in 24 out of 38 patients (63.2%), with p.D538G and p.Y537S being the most common alterations. Lung metastases were significantly more common in ESR1-mutant cases (33.3%) compared with wildtype cases (7.1%), while liver metastases showed no difference between groups (50.0% in both). Comutations in actionable pathways, particularly PIK3CA, were observed in 10 ESR1-mutant tumors (41.6%), highlighting the complexity of resistance mechanisms and posing challenges for treatment selection, as these alterations might necessitate combination therapies. The study showed that FFPE biopsy samples from metastatic sites can serve as a viable alternative for ESR1 mutation detection.
* PMID: 40369610, PMCID: PMC12079830
Assessment of ESR1, PGR, ERBB2, and MKI67 mRNA in hormone receptor–positive early breast cancer
Rezvani H, Forghani S, Forghani A, et al. Health Sci Rep. 2025;8(7):e71062.
Summary. This cross-sectional study evaluated the concordance between quantitative reverse transcription polymerase chain reaction (PCR) and immunohistochemistry (IHC) for assessing ER, progesterone receptor (PR), HER2, and Ki-67 in 145 hormone receptor–positive (HR+) early breast cancer samples. The overall concordance between messenger ribonucleic acid (mRNA) expression and IHC was 95.9 percent for ESR1/ER, 79.3 percent for PGR/PR, and 100 percent for ERBB2/HER2, while a moderate correlation was found between MKI67 mRNA and Ki-67 IHC (r=0.34, p<0.001). ESR1 mRNA expression was significantly lower in patients aged 60 years or younger compared to those older than 60 years (p<0.001), whereas no significant association was found between age at diagnosis and ER IHC (r=0.12, p=0.16). Higher ESR1 mRNA expression was associated with increased tumor size, more lymph node involvement, and higher stage, while higher MKI67 mRNA expression correlated with increased tumor size and higher stage. These findings suggest that PCR-based classification performed in a central laboratory might serve as a complementary method to confirm IHC results from local laboratories and provide additional valuable information for patient management, potentially offering a more standardized approach to breast cancer biomarker assessment.
* PMID: 40666735, PMCID: PMC12261032
Genomic landscape of hormone therapy-resistant HR+, HER2– breast cancer
Chaubal R, Talker E, Chitra J, et al. Breast Cancer Res Treat. 2025;213(2):247–259.
Summary. This study characterized the genomic landscape of HR+, HER2– breast cancer in patients with hormone therapy–resistant and hormone therapy–sensitive disease. Whole-exome sequencing (WES) was performed on paired treatment-naïve and relapse-site tumor samples along with germline deoxyribonucleic acid (DNA) from 19 hormone therapy–resistant patients, while targeted NGS was performed on circulating tumor DNA (ctDNA) from 35 resistant and 19 sensitive patients. Among the 19 resistant patients, mutational burden was significantly higher at relapse compared with treatment-naïve samples (median 0.883 vs. 0.655 mutations/megabase, p=0.03), 64 driver mutations were identified (median 2 per treatment-naïve sample vs. 3 per relapse sample), and 21 mutations in eight genes were classified as actionable in 15 (78.9%) patients. Branching evolutionary trajectories were observed in 18 (94.7%) patients, with PIK3CA and/or TP53 mutations present in stem clones of 13 (68.4%) patients. In the ctDNA analysis of 35 resistant patients, 27 actionable hotspot mutations were identified in 25 (71.4%) patients. The findings demonstrate that hormone therapy–resistant HR+/HER2– negative breast cancers are polyclonal, acquire actionable alterations at relapse, and that moderate-depth ctDNA sequencing can successfully identify many clonal mutations.
* PMID: 40652157, PMCID: PMC12331804
Clinical impact of single-gene vs. panel sequencing in advanced HR+, HER2– breast cancer
Klocker EV, Dobrić N, Graf R, et al. NPJ Breast Cancer. 2025;11(1):86.
Summary. This prospective, multicenter study compared single-gene (SiMSen-Seq, SSS) and panel-based sequencing (AVENIO ctDNA Expanded assay, 77 genes) for detecting PIK3CA mutations and broader genomic profiling in 161 plasma samples from 146 patients with HR+, HER2− breast cancer before initiating palliative therapy. High concordance (92.6%) was observed between SSS and AVENIO for PIK3CA mutation detection, with positive percent agreement (PPA) of 88.7 percent and negative percent agreement (NPA) of 94.3 percent. The AVENIO assay identified additional actionable PIK3CA mutations not covered by SSS in 18.6 percent of cases, with 9.4 percent of patients potentially missed by SSS alone. Beyond PIK3CA, AVENIO detected clinically relevant mutations in ESR1 (17.5% of patients), with D538G and Y537S being the most common variants, and PI3K pathway alterations in 40.6 percent of samples. ESR1 mutations were significantly more frequent in second-line compared with first-line samples (p=0.002), and polyclonal mutations in both ESR1 and PIK3CA were more common in second-line samples. Combining tumor fraction estimation (z-score ≥3 or highest variant allele frequency [hVAF] ≥1%) with panel sequencing improved classification of negative liquid biopsy results, identifying 52.7 percent of PIK3CA wildtype samples as informative true negatives. The findings support the clinical utility of broader ctDNA profiling using panel-based approaches to identify actionable mutations, monitor resistance mechanisms, and improve interpretation of negative results.
* PMID: 40775238, PMCID: PMC12331942
Genomic and clinical features in young women with ER+, HER2– breast cancer
Walbaum B, Martínez-Sáez O, Brasó-Maristany F, et al. ESMO Open. 2025;10(10):105764.
Summary. This study examined genomic and clinical features of young women (≤40 years) with ER+, HER2− early breast cancer compared with older patients (41–50 years and >50 years) using Prediction Analysis of Microarray 50 (PAM50)/Prosigna testing in 658 patients. Young women presented with more aggressive disease characteristics, including larger tumors, higher Ki-67 proliferation indices, and more frequent low ER expression. IHC-based luminal A-like tumors were less common in young women, while luminal B intrinsic subtype by PAM50 was more prevalent. Critically, conventional biomarkers showed poor concordance with genomic risk in young women, as 26.3 percent of IHC luminal A-like tumors were reclassified as luminal B by PAM50; additionally, 50 percent of tumors with Ki-67 less than 10 percent had high-risk risk of recurrence (ROR) scores, compared with only 4.7 percent and 4.5 percent in older groups. Five-year disease-free survival (DFS) was significantly lower in young women, with particularly poor outcomes among IHC luminal A-like tumors. ROR score remained independently prognostic in young women in multivariable analysis. Gene expression profiling revealed that young women had significantly lower expression of estrogen-related genes and higher expression of proliferation-associated genes. These findings demonstrate that young women with ER+, HER2− early breast cancer harbor distinct tumor biology and support the need for genomic profiling and age-specific treatment strategies in this high-risk population.
*PMID: 40997745, PMCID: PMC12495081