Molecular and prognostic convergence of HR+/HER2– metastatic breast cancer (MBC) to a TNBC-like profile: Insights from circulating tumor DNA (ctDNA)-based genomic analysis across treatment lines

Background: While the transition to a triple negative (TNBC)-like profile represents a recognized mechanism of treatment resistance for hormone receptor-positive, HER2-negative (HR+/HER2-) MBC, the molecular mechanisms of this phenomenon remain largely unknown. This analysis investigated the genomic and prognostic differences between HR+/HER2– and TNBC across treatment lines through ctDNA profiling analysis Methods: This retrospective study analyzed a multi-institutional cohort of 1071 patients (pts) with HER2 negative MBC and ctDNA testing with the Guardant360 NGS panel within a large academic consortium (PMAC). HR and HER2 status were defined based on the most recent biopsy, pts with ER-low profile (ER < 10% regardless of PR status) were excluded. Associations across single nucleotide and copy number variations (SNVs and CNVs), HR+/HER2– and TNBC subtypes across treatment lines were tested by multinomial logistic regression (MLR) in terms of Relative Risk Ratio (RRR). The impact of prognosis was evaluated through Cox regression for overall survival (OS), defined from time of baseline ctDNA collection. Results: There were 827 pts with HR+/HER2- MBC (77.2%) and 244 pts with TNBC (22.8%). Multivariable MLR, designed with first line HR+/HER2- as the reference, investigated genomic alterations across treatment lines. In second line, ESR1 SNVs (RRR 7.34, p < 0.001) and EGFR CNVs (RRR 0.15, p = 0.01) were significantly associated with HR+/HER2-, while TP53 SNVs had a higher prevalence in TNBC (RRR 2.71, p = 0.009). In third line, ESR1 SNVs were significantly enriched in HR+/HER2- (RRR 5.44, p < 0.001), while TP53 SNVs emerged for TNBC (RRR 5.26, p < 0.001). From fourth line onward (≥ 4L), ESR1 SNVs (RRR 8.09, p < 0.001), TP53 SNVs (RRR 1.81, p = 0.022) and PIK3CA CNVs (RRR 5.93, p = 0.003) showed higher prevalence in HR+/HER2- relative to first line HR+/HER2-, while TP53 SNVs were also associated with TNBC (RRR 10.43, p < 0.001). Compared to TNBC, HR+/HER2– had a favorable prognostic impact in terms of OS in first (HR 0.32, p < 0.001), second (HR 0.35, p < 0.001) and third line (HR 0.37, p < 0.001). However, in ≥ 4L, no significant differences emerged (HR 0.79, p = 0.282), with similar results observed with respect to TNBC across all lines (HR 1.01, p = 0.929). MYC CNVs had an unfavorable prognostic role for both HR+/HER2− ≥4L (HR 2.41, p = 0.004) and TNBC in all lines (HR 2.14, p = 0.014). Conclusions: Our study suggests a dynamic molecular evolution of HR+/HER2– MBC, with a progressive acquisition of molecular and prognostic features compatible with a TNBC-like profile and loss of endocrine sensitivity. These findings highlight the need for comprehensive biological characterization of this subtype across treatment lines to better understand its evolution under therapeutic pressure and consequently adapt treatments.