TRLS-09 Cerebrospinal Fluid (Csf) and Plasma Circulating Tumor Dna (Ctdna) for Molecular Profiling and Monitoring of Treatment Response in a Phase Ii Trial of Paxalisib for Her2-Positive (Her2+) Breast Cancer Brain Metastases (Bcbm)

Up to half of patients with HER2+ metastatic breast cancer (MBC) develop brain metastases (BM), leading to significant morbidity and reduced survival. Yet, genomic characterization of BM remains limited. Plasma-ctDNA has low sensitivity for brain disease. CSF-ctDNA may better reflect the genomic landscape of central nervous system (CNS) tumors, potentially serving as a better biomarker. Here, we analyzed ctDNA from CSF and plasma samples collected in a phase II trial (NCT03765983) evaluating paxalisib, a brain-penetrant PI3K/mTOR inhibitor, plus trastuzumab in patients with active/progressive HER2+ BCBM. Patients with LMD were excluded. Ultra-low-pass whole-genome sequencing (ULP-WGS) and whole-exome sequencing (WES) were performed. Among 5 patients with WES (10 samples: 7 CSF, 3 plasma), genomic alterations were consistent with HER2+ MBC, including ERBB2 amplification (4/5), TP53 (3/5), PIK3CA (2/5) and PTEN (1/5) mutations. MYC and proliferation-related copy number alterations were frequent (3/5). The only patient with clinical benefit (RANO-BM SD>24 weeks) lacked PIK3CA pathway mutations. ULP-WGS was performed at baseline and cycle 2 day 1 in 8 patients with paired plasma and 5 patients with paired CSF samples. Baseline tumor fraction (TF) was consistently higher in CSF than plasma (median TF 0.56 vs 0.03). CSF TF dynamics correlated with CNS target lesion changes: 3/5 patients with declining TF had tumor shrinkage (though none met RANO-BM criteria for PR), while 2 with increasing TF had increase or were unevaluable. The patient with clinical benefit had the most pronounced TF decline (0.58 to 0.08). CSF clonal evolution (|△CCF|>0.20) was observed in two patients, including the clinical benefit patient, who exhibited the strongest dynamics. Phylogenetic analysis in one patient showed shared truncal mutations in plasma and CSF, with a CSF subclone of low clonality in plasma. These findings suggest that CSF-ctDNA may better capture tumor genomics and treatment response than plasma-ctDNA in HER2+ BCBM.