Figure 1.

Systematic mapping of CDK gene function in triple negative breast cancer cells. (a) CDK proteins control cell-cycle progression and act as transcriptional regulators, garnering interest as potential drug targets (colors). (b) Schematic describing the combinatorial CRISPR/Cas9 fitness screening approach to map CDK synthetic-lethal and synergistic interactions. A library of dual sgRNA constructs targeting pairs of genes listed in (a) was synthesized as an oligonucleotide pool and cloned into a lentiviral overexpression vector (top). TNBC cell lines were transduced with virus coding for this library and subjected to competitive growth screening. Resulting dual sgRNA construct fitnesses were used to extract single gene fitness values and map genetic interactions. (c) Schematic describing the single-cell transcriptional phenotyping approach to map the functional impact of CDK genetic perturbations. An sgRNA library targeting the genes in (a) was cloned into an scRNA-seq-compatible lentiviral overexpression vector and used to transduce TNBC cell lines in pooled format. One week after transduction, scRNA-seq was performed using the 10x Chromium platform.