PALOMA-2 Data Request for Biomarker Analysis

The CDK4/6 (cyclin-dependent kinase 4/6) inhibitor such as palbociclib has shown significant efficacy in treating breast cancer. However, patients do not exhibit a unformal response, and the underlying resistance/sensitivity mechanism remains incompletely understood. In this proposal, we will apply genome-wide CRISPR/Cas9 screen techniques to categorize the range of genetic alterations that confer resistance or sensitivity to CDK4/6 inhibitors, and seek validation through analysis of genomic and expression data of breast cancers treated by palbociclib. The conclusion of this research may help inform the personalized use of palbociclib to increase treatment efficacy. It will also shed light on the resistance mechanism for relapsed cases and point to potential means to avert or reverse such resistance.
Treatment of cancer cells with palbociclib often results in cytostatic response in tissue culture. Cells stop proliferation under such conditions, but do not undergo cell death. This increased the difficulty to conduct genome-wide screen, which performs best when drug causes significant cell death, and the resistant clones repopulate tissue culture. We have found a cell line that undergoes quick cell death in response to palbociclib at low micromolar concentration. The cell line is very suitable for interrogating the genetic determinants of drug response (Ding et al Cell Reports 2019, Pubmed ID 31189115). Using this system, we introduced genome-wide sgRNA library into the cells, and was able to examine which genes, when edited by CRISPR/Cas9, cause resistance or sensitivity to palbociclib. On average 15 sgRNAs were used to cover each gene, and the data quality suggested that we have achieved a very good palbociclib genome-wide screen. In following up studies, we will aim to analyze the genomic and expression data of palbociclib-treated cancers, focusing on the set of resistance and sensitivity gene sets discovered by our screen. For genes that can significantly separate good and poor response cases, we will study the underlying molecular mechanism. This study may help expand our understanding of the clinical efficacy of CDK4/6 inhibitors and aid their precision use in clinic.