Leilani Anderson

Supplementary tables 1-4 and supplementary figure legend

Supplemental Figure 6: Evolutionary analysis of longitudinal plasma ctDNA samples

Supplemental Figure 1: Consort diagram

Supplemental Figure 5: SSNVs detected in the cancer-related genes across 68 ctDNA WES samples

Supplemental Figure 2: Plasma circulating tumor DNA (ctDNA) collection and analysis

Supplemental Figure 3: Plasma circulating tumor DNA (ctDNA) tumor fraction (TF) dynamics determined with ULP-WGS

Supplemental Figure 4: Overview of SSNVs in 68 ctDNA WES samples

Purpose:Sensitivity to endocrine therapy (ET) is critical for the clinical benefit from the combination of palbociclib plus ET in hormone receptor–positive/HER2-negative (HR+/HER2−) advanced breast cancer. Bazedoxifene is a third-generation selective estrogen receptor (ER) modulator and selective ER degrader with activity in preclinical models of endocrine-resistant breast cancer, including models harboring ESR1 mutations. Clinical trials in healthy women showed that bazedoxifene is well tolerated.Patients and Methods:We conducted a phase Ib/II study of bazedoxifene plus palbociclib in patients with HR+/HER2− advanced breast cancer who progressed on prior ET (N = 36; NCT02448771).Results:The study met its primary endpoint, with a clinical benefit rate of 33.3%, and the safety profile was consistent with what has previously been seen with palbociclib monotherapy. The median progression-free survival (PFS) was 3.6 months [95% confidence interval (CI), 2.0–7.2]. An activating PIK3CA mutation at baseline was associated with a shorter PFS (HR = 4.4; 95% CI, 1.5–13; P = 0.0026), but activating ESR1 mutations did not impact the PFS. Longitudinal plasma circulating tumor DNA whole-exome sequencing (WES; N = 68 plasma samples) provided an overview of the tumor heterogeneity and the subclonal genetic evolution, and identified actionable mutations acquired during treatment.Conclusions:The combination of palbociclib and bazedoxifene has clinical efficacy and an acceptable safety profile in a heavily pretreated patient population with advanced HR+/HER2− breast cancer. These results merit continued investigation of bazedoxifene in breast cancer.

Supplemental Figure 6: Evolutionary analysis of longitudinal plasma ctDNA samples