Single cell DNA sequencing reveals clonal selection, hormonal adaptation and treatment resistance in neoadjuvant clinical trial of Aromatase inhibition

Background. The aromatase inhibitors (AI) letrozole and exemestane are often used in sequence in targeting ER+ breast cancers. However, resistance to AI poses a major barrier to sustained clinical benefit, while the biological mechanisms underlying the phenomenon remain largely unknown. In this study, we build on our clinical NeoLetExe trial, with the aim to investigate the molecular basis of resistance to AI, by analysing subclonal evolutionary dynamics during sequential treatment. Methods. We use whole-exome sequencing (WES) data from 11 ER + breast cancer patients and 3 timepoints of the Neoletexe trial to reconstruct cancer cell fraction-based subclonal composition. Single-cell DNA sequencing from matched tumour samples is generated on the MissionBio platform to validate the identified clones and variants. Subclonal variants were annotated to genes by integrating evidence from public data and ExpectoSc. Pathway enrichment analysis using Human Base was conducted. Results. Higher cancer cell fraction clone trajectories were significantly associated with reduced treatment response (p = 0.023). Clones reconstructed by WES were validated at 81% using single-cell DNA sequencing. Clones resistant to both letrozole and exemestane demonstrated PIK3CA/AKT/mTOR signaling activation, KRAS pathway dysregulation, hedgehog signaling, and androgen receptor pathways, alongside extensive immune activation and metabolic reprogramming. Drug-specific resistance patterns showed exemestane-resistant clones enriched for epigenetic control and miRNA-mediated silencing, while letrozole-resistant clones displayed metabolic dysregulation but notably lacked immune pathway activation. In contrast, treatment-sensitive clones maintained coordinated cell cycle control, preserved DNA damage responses, and retained immune signaling capacity. Analysis of FDA-approved breast cancer targets identified actionable alterations in PIK3CA (4 patients) and AKT1 (1 patient) that persisted through AI treatment, with RNA expression analysis revealing 48 additional therapeutic targets spanning PI3K/AKT/mTOR, CDK4/6, DNA repair (BRCA1/2, ATM), and immune checkpoint pathways. Conclusion. WES-based cancer cell fraction analysis successfully captured subclonal evolutionary trajectories during AI treatment, revealing drug-specific mechanisms and identifying key molecular players in endocrine therapy resistance. This work establishes a framework for precision oncology approaches by providing actionable therapeutic targets and advancing our understanding of resistance mechanisms to improve clinical outcomes in sequential AI therapy.