Analysis of single cells treated with the KRASG12D inhibitor MRTX 1133 reveals new challenges for the emerging field of single cell proteomics

Abstract

Mutations in KRAS are common drivers of human cancers and are often those with the poorest overall prognosis for patients. A recently developed compound, MRTX1133 has shown promise in inhibiting the KRASG12D mutant protein, which is a primary driver mutation in pancreatic cancer cases worldwide. In this study, I performed a multi-omic analysis of four cancer cell lines following acute treatment with this compound. To obtain increased granularity in the observed proteomic observation, I attempted to perform multiplexed single cell proteomics on all four cell lines with a goal of over 500 single cells per treatment condition. Due to a high level of cellular death and morphological changes induced in the two mutant cell lines following drug treatment, only two cell lines could be analyzed with this approach. The final results provided in this draft contain results from approximately 1,800 single cells from two cell lines which each harbor two copies of the KRASG12D mutant gene. From these files 3,140 total proteins were identified with approximately 953 proteins quantified per cell. These results were sufficient to differentiate between single pancreatic cancer cells derived from different patients. In addition, I present observations suggesting new challenges to consider in pharmacological applications for single cell proteomics, including biases related to how the carrier channels are prepared and how single cells are selected or aliquoted. By sorting for viable cells following drug treatment that leads to high levels of cell death, I obtain very different results than when the entire populations are homogenized for bulk proteomics.