PIK3CA and KRAS codon-specific mutations differentially toggle pathway activity and alter sensitivity to inavolisib (GDC-0077)

To explore the single and combinatorial effect of MEK and PI3KCA inhibitors in CRC lines with PIK3CA/KRAS mutations, we used the MULTI-seq CMOs to perform a highly multiplexed single-cell RNA-seq. Overall design: Four different CRC lines, GP2d, LS174T, T84 and HCT116 were treated with either with single drug or the combinations. We harvested the cells at 24 hours and 96 hours after the treatment. Two biological duplicates were collected for each condition, and in total there are 64 samples. Upon harvesting, we trypsinized all the cells and labelled each sample with a unique CMO tag. After that, every 32 samples from the same biological duplicate were combined into one cell pool (two pools in total) and a FACS was performed on each pool to get rid of the dead cells. Eventually, we loaded each cell pool on 3 10X Genomics 3' scRNA-seq lanes and a total of 6 runs were performed. In this project, there are 6 transcriptome libraries and 6 corresponding CMO libraries. The results from T84 cell lines showed that they were of low quality and they were removed from CountMatrix.mtx and Metadata.txt Please note that each sample represents mixed sample, multiplexed experiment and that the barcode labels for demultiplexing are included as a supplemental file along with the cell assignment.