Publications

Multiplexed and reproducible high content screening of live and fixed cells using the Dye Drop method (2021)
Abstract: High throughput measurement of cell perturbation, by libraries of small molecules or gene knockouts, is a key step in functional genomics and pre-clinical drug development. However, it is difficult to perform viable, single-cell assays in 384-well plates, limiting many studies to simple well-average measurements (e.g. CellTiter-Glo®). Here we describe a public domain “Dye Drop” method in which sequential density displacement is used to perform multi-step assays for cell viability and EdU incorporation followed by immunofluorescence imaging. The method is rapid, reproducible, can be readily customized, and is compatible with either manual or automated laboratory equipment. We demonstrate Dye Drop in the collection of dose-response data for 67 drugs in 58 breast cancer cell lines and separate cytostatic and cytotoxic responses, thereby providing new insight into the effects of specific drugs on cell cycle progression and cell viability. Dye Drop substantially improves the tradeoff between data content and cost, enabling collection of large information-rich datasets.
DOI: https://doi.org/10.1101/2021.08.27.457854
 
Data Descriptor: Proteomic profiling across breast cancer cell lines and models (2020)
Abstract: We performed quantitative proteomics on 61 human-derived breast cancer cell lines to a depth of ~13,000 proteins. The resulting high-throughput datasets were assessed for quality and reproducibility. We used the datasets to identify and characterize the subtypes of breast cancer and showed that they conform to known transcriptional subtypes, revealing that molecular subtypes are preserved even in under-sampled protein feature sets. All datasets are freely available as public resources on the LINCS portal. We anticipate that these datasets, either in isolation or in combination with complimentary measurements such as genomics, transcriptomics and phosphoproteomics, can be mined for the purpose of predicting drug response, informing cell line specific context in models of signalling pathways, and identifying markers of sensitivity or resistance to therapeutics.
DOI: https://doi.org/10.1101/2020.12.15.422823
 
Development of CDK2 and CDK5 Dual Degrader TMX-2172 (2020)
Abstract: Cyclin-dependent kinase 2 (CDK2) is a potential therapeutic target for the treatment of cancer. Development of CDK2 inhibitors has been extremely challenging as its ATP-binding site shares high similarity with CDK1, a related kinase whose inhibition causes toxic effects. Here, we report the development of TMX-2172, a heterobifunctional CDK2 degrader with degradation selectivity for CDK2 and CDK5 over not only CDK1, but transcriptional CDKs (CDK7 and CDK9) and cell cycle CDKs (CDK4 and CDK6) as well. In addition, we demonstrate that antiproliferative activity in ovarian cancer cells (OVCAR8) depends on CDK2 degradation and correlates with high expression of cyclin E1 (CCNE1), which functions as a regulatory subunit of CDK2. Collectively, our work provides evidence that TMX-2172 represents a lead for further development and that CDK2 degradation is a potentially valuable therapeutic strategy in ovarian and other cancers that overexpress CCNE1.
DOI: doi.org/10.1002/ange.202004087
 

 

 

Multiplexed and Reproducible High Content Screening of Live and Fixed Cells Using the Dye Drop Method7.41 MB
Data Descriptor Proteomic Profiling Across Breast Cancer Cell Lines and Models14.38 MB
Development of CDK2 and CDK5 Dual Degrader TMX-21721.15 MB