Clinical Efficacy and Whole-Exome Sequencing of Liquid Biopsies in a Phase IB/II Study of Bazedoxifene and Palbociclib in Advanced Hormone Receptor-Positive Breast Cancer

Abstract

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.

Figure 1.

Efficacy of bazedoxifene and palbociclib in evaluable patients. A. Swimmer plot of 34 patients evaluable for time to event end points. Vertical dotted line indicates 6 months. The left panel denotes patients who have liver metastases (liver mets) in red, the number of organs involved with metastases (Number of mets), number of lines of treatment in the metastatic setting (patients who had not received treatment in metastatic disease developed disease recurrence during or within 1 year of adjuvant ET), prior fulvestrant (Fulv) treatment indicated in green and prior chemotherapy treatment indicated in blue (Chemo). † denotes patient 28 who stayed on treatment for 18 cycles despite of the PD assessment after cycle 2. ‡ denotes patient 29 who stayed on treatment for additional 14 days after the last disease evaluation. Neither patient 28 nor patient 29 is considered as having clinical benefit. B. Waterfall plot with best percentage of tumor changes from baseline sum of the longest diameter in target lesions of the 34 evaluable patients. Response is based on RECIST 1.1 criteria. Horizontal dotted line indicates −30% change of targeted lesion. C. Kaplan-Meier curve representing progression-free survival (PFS) for intention to treat patient population (n=36). Median PFS 3.6 months, 95% CI: 2-7.2 months. D. Kaplan-Meier curve representing overall survival (OS) for the intention to treat patient population (n=36). Median OS 26.5 months (95% lower confidence limit 20.7 months). Abbreviations: PD, progressive disease; PR – partial response; SD – stable disease

Figure 2:

Whole exome sequencing. A. Baseline somatic mutations in cancer-related genes detected by ctDNA whole exome sequencing (WES) (n=28) in at least two patients. B. Lollipop diagram denoting the ESR1 mutations detected in the baseline ctDNA samples. C. Lollipop diagram denoting the PIK3CA mutations detected in the baseline ctDNA samples. D. Kaplan-Meier curve representing progression-free survival (PFS) during treatment with palbociclib and bazedoxifene in patients with baseline ctDNA WES stratified by no/yes baseline ESR1 ctDNA mutation. The median PFS for patients with WT (wild-type) ESR1 versus mutant ESR1 is 3.6 months and 2 months, respectively. HR = 1.0 (95% CI: 0.4 – 2.4); P = 0.94; log-rank test. E. Kaplan-Meier curve representing PFS on treatment for patients with baseline WES ctDNA analysis stratified by no/yes baseline ctDNA PIK3CA mutation. The median PFS for patients with WT PIK3CA versus mutant PIK3CA was 3.9 months versus 1.8 months, respectively. HR= 0.2 (95% CI: 0.06-0.6); P=0.0019, log-rank test. F. Kaplan-Meier curve representing PFS on treatment for patients with baseline WES ctDNA analysis stratified by no/yes baseline ctDNA truncating mutation. The median PFS for patients without a truncating mutation versus with a truncating mutation was 3.8 months versus 1.7 months, respectively. HR = 0.3 (95% CI 0.1-0.7); P=0.0059, log-rank test. G. End of treatment (EOT) somatic mutations in cancer-related genes detected by ctDNA whole exome sequencing (WES) (n=22) in at least two patients. H. Correlation of the frequency of mutations in cancer-related genes that were detected in at least two patients and including patients with matched baseline and EOT treatment ctDNA WES (n= 20), r=0.7, P=0.01, Pearson correlation. Abbreviations: ctDNA – circulating tumor DNA

Figure 3:

Copy number variations, tumor mutational burden (TMB), and mutational signatures. A. Somatic copy number variations (amplifications (AMP), gains, loss, and neutral loss of heterozygosity) in cancer-related genes detected in at least two patients. Samples are from 16 patients and include matched samples from at least two time points (baseline, C2D1 (cycle 2 day1) and end of treatment (EOT)) in 9 patients. B. Serial TMB at baseline (n=28), cycle 2 day1 (C2D1) (n=18), and end of treatment (EOT) (n=22). C. Mutational signatures detected in cfDNA samples. Abbreviations: cfDNA – cell-free DNA

Figure 4:

Evolutionary analysis of longitudinal plasma ctDNA samples. A-D. Left panel showing the phylogenetic trees representing the clonal architecture in plasma ctDNA samples. The number of somatic alterations assigned to each clone and detected alterations in known cancer genes are denoted in each branch. A-D. right panel showing the estimated cancer cell fraction (CCF) of each clone at baseline, after 1 cycle of treatment (C2D1) and end of treatment (EOT). The color of the clone matches the respective clone in the phylogenetic trees. * denotes truncating mutations Abbreviations: ctDNA – circulating tumor DNA