Abstract P3-05-18: Prognostic value of ctDNA dynamics and protein biomarkers in patients treated with alpelisib (ALP) and endocrine therapy (ET) for HR+/HER2- PIK3CA-mutated advanced breast cancer (ABC) in all 3 cohorts of the phase II BYLieve study

Abstract Background: The BYLieve study demonstrated efficacy and safety of ALP (PI3K-α inhibitor and degrader) + ET in patients (pts) with PIK3CA-mutated HR+/HER2− ABC post-progression of treatments including cyclin-dependent kinase 4/6 inhibitor (CDK4/6i). We assessed the prognostic role of ctDNA dynamics and protein biomarkers in pts from this study. Methods: Pts on prior immediate treatment of CDK4/6i + aromatase inhibitor (AI, Cohort A, n=101), and AI followed by chemotherapy/ET (Cohort C, n=98) receiving ALP + fulvestrant and prior immediate treatment of CDK4/6i + fulvestrant receiving ALP + letrozole (Cohort B, n=97) were included for biomarker analysis. ctDNA fraction levels for samples collected at baseline (BL; Cycle 1, Day 1 [C1D1]) and at end-of-treatment (EOT) were analyzed using cfDNA 2.0 assay for all 3 Cohorts and samples collected at C2D1 (only for Cohort A & B) were analyzed using cfDNA 2.1 assay, both utilizing PanCancer analysis panel that covered coding exons of 579 genes. Genomic landscape alterations in Pi3K/AKT pathway and potential CDK4/6i resistance markers were assessed across those time points. Circulating proteins from a selection of matched patient/timepoint samples (Cohorts A, B and C, n=578) were assessed via SomaScan, an exploratory proteomics platform profiling 7,596 proteins from a single plasma blood sample. The association between ctDNA fraction and protein markers (SOMAmers) was assessed for all matched samples and the prognostic value of identified enriched SOMAmers was investigated at BL (all cohorts, n=292). Results: Among pts who had matched samples at C1D1 and C2D1, 15 of 82 in Cohort A and 11 of 80 in Cohort B had ctDNA fraction=0 at BL. In pts with ctDNA fraction >0 at C1D1, ALP treatment led to a rapid decrease in median ctDNA fraction at C2D1 in Cohort A (C1D1, 0.1; C2D1, 0.055; P=0.023) and Cohort B (C1D1, 0.126; C2D1, 0.079; P=0.044). No significant differences were observed in gene mutation frequencies (including ESR1 and TP53 mutations) across timepoints, in both cohorts, except the Pi3K/AKT pathway-related genes (AKT1,2,3, PIK3R1, PTEN) that revealed an increased number of alterations at EOT. The alterations in genes implicated in CDK4/6i resistance (CDKN2A, CDKN2B, RB1, PIK3R1, ERBB2, FAT1, NF1, CHD4) were consistent in both pt cohorts, but caution needed to interpret this due to limited sample size. Pts in Cohort A, with ctDNA fraction >0 at C1D1 and C2D1 had shorter PFS vs pts with undetectable ctDNA at C2D1 (P<0.0001). Correlation analysis between circulating proteins and ctDNA fraction at BL from matched samples revealed significant enrichment for SOMAmers positively (n=858) and negatively (n=316) correlating with ctDNA fraction. The top enriched SOMAmers for positive correlation with ctDNA fraction exhibited significant predictive value for poor PFS (P<0.0001), while the top enriched SOMAmers for negative correlation showed significant predictive value for favorable PFS (P<0.0001); both with comparable predictive value to ctDNA fraction. The combination of ctDNA fraction and protein signal at BL provided better prediction of PFS compared to either measurement independently. Identified SOMAmers also show evidence of further discrimination of PFS response in pts with ctDNA fraction=0. Conclusions: ctDNA fraction reduction at early timepoints demonstrates rapid and early response of ALP treatment in PIK3CA-mutated HR+/HER2– ABC. With the exception of Pi3K/AKT pathway-related genes, we observed consistency in alterations, especially in genes implicated in CDK4/6i resistance across timepoints suggesting that ALP does not alter overall tumor biology. Notably, an increase in alterations within Pi3K/AKT pathway genes at EOT may indicate a potential resistance mechanism and provide guidance on next lines of therapy The SomaScan analysis highlights independent value of circulating protein markers and their complementarity with ctDNA fraction, suggesting their prognostic value. Citation Format: Dejan Juric, Yoon-Sim Yap, Stephen Chia, Sherene Loi, Fabrice André, Nicholas Turner, Patrick Neven, Eva M. Ciruelos, Sara M. Tolaney, Jessica Makofske, Mukta Joshi, Estelle Roux, Murat Akdere, Hope S. Rugo. Prognostic value of ctDNA dynamics and protein biomarkers in patients treated with alpelisib (ALP) and endocrine therapy (ET) for HR+/HER2- PIK3CA-mutated advanced breast cancer (ABC) in all 3 cohorts of the phase II BYLieve study [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P3-05-18.