Lead Investigator: C Elizabeth Caldon, Garvan Institute of Medical Research
Title of Proposal Research: Therapeutic targeting of dual CDK4/6 inhibitor and endocrine resistant breast cancer
Vivli Data Request: 4541
Funding Source: National Breast Cancer Foundation (IIRS-19-054)
Potential Conflicts of Interest: None
Summary of the Proposed Research:
Approximately 75% of all breast cancers express estrogen receptor (ER), and receive adjuvant endocrine therapy, but ~35% of these patients recur with endocrine therapy resistant disease. Once metastatic, endocrine resistant breast cancer is incurable and contributes to >50% of breast cancer deaths [1]. The recent introduction of CDK4/6 inhibitors offers these patients a next line of therapy. Combination therapy of CDK4/6 inhibitors with endocrine therapy has doubled the progression free survival of patients with advanced ER-positive breast cancer in seminal phase 3 studies, and is now FDA approved for use in the first line setting [2-5]. It is expected that most ER-positive breast cancer patients in countries with CDK4/6 inhibitors therapy approval will receive endocrine therapy and CDK4/6 inhibitors during the course of their treatment.
In our proposal, we use endocrine therapy and CDK4/6 inhibitor resistance models, in vitro and in vivo, to discover new therapeutic targets by identifying the mechanisms of resistance. We aim to validate which of these mechanisms are unique to single agent and/or combination therapy by comparing both the mono- and dual-therapy resistance models, and expand the comparison across publicly cohorts, including Turner et al. (2019) (GEO accession GSE128500) [2], on endocrine therapy and CDK4/6 inhibitor trial. We will subsequently perform pre-clinical screening of new therapeutic regimes to identify tailored treatments for dual resistant advanced ER-positive breast cancer. This will lead to major impact on the practice of personalised medicine, with trials that rapidly accelerate the progress of breast cancer management and advance sourcing support for further innovative clinical interventions in Australia and worldwide.
Statistical Analysis Plan:
We aim to perform a meta-analysis using the dataset published by Turnet et al. (2019) [2], GEO accession GSE128500, in line with the outcome data from the PALOMA-3 trial (NCT01942135), including patient treatment information and progression-free survival data. We will use this data to validate biomarkers and molecular pathways that change with combination therapy (palbociclib plus fulvestrant), and importantly, identify potentially targetable resistance mechanisms to single and dual therapy resistance. This will allow us to establish the appropriate context of subsequent analysis in resistant in vitro and in vivo models developed at the Garvan Institute of Medical Research.
The hypothesis-driven analysis will be conducted on the gene signature identified from the gene expression, gene set enrichment and KEGG pathway analysis performed in our in vivo and in vitro models. Varying levels of individual genes and the signature will be compared across subpopulation treatment arms (palbociclib plus fulvestrant or placebo plus fulvestrant) and progression-free survival (PFS) in the GSE128500 targeted sequencing data, as part of the PALOMA-3 trial (NCT01942135). Data analyses will be performed using R (www.r-project.org) and Bioconductor packages. We will use the R environment to normalize (quantile normalization and log2 transformation) gene expression values and to perform statistical tests on subpopulation treatment effects (Student’s t-test) and among independent samples (Wilcoxon’s rank-sum test). Survival analysis (Cox proportional hazards regression) will be performed to investigate the association between gene levels and treatment effects, in terms of progression-free survival (PFS), adjusted using the false discovery rate (FDR) method.
Requested Studies:
Palbociclib (PD-0332991) Combined With Fulvestrant In Hormone Receptor+ HER2-Negative Metastatic Breast Cancer After Endocrine Failure (PALOMA-3) Description: 521 endocrine-pretreated patients that receive palbociclib plus fulvestrant or placebo plus fulvestrant
Sponsor: Pfizer
Study ID: NCT01942135
Summary of Results:
We were unable to bring our analysis to completion as we believe that the dataset was too small and/or the patient population too variable to observe significant differences in our analysis.