Comparative Transcriptomic Analysis of aKO and p-aKO in Pancreatic Cancer Cells

Most human pancreatic ductal adenocarcinoma (PDAC) are not infiltrated with cytotoxic T cells and are highly resistant to immunotherapy. Over 90% of PDAC have oncogenic KRAS mutations, and phosphoinositide 3-kinases (PI3Ks) are direct effectors of KRAS. Our previous study demonstrated that ablation of Pik3ca in KPC (KrasG12D; Trp53R172H; Pdx1-Cre) pancreatic cancer cells induced host T cells to infiltrate and completely eliminate the tumors in a syngeneic orthotopic implantation mouse model. This study now shows that implantation of Pik3ca-/- KPC (named αKO) cancer cells induces clonal expansion of cytotoxic T cells infiltrating the pancreatic tumors in this mouse model. To identify potential molecules that can regulate the activity of these anti-tumor T cells, we conducted an in vivo genome-wide gene-deletion screen using αKO cells implanted in the mouse pancreas. The result shows that deletion of propionyl-CoA carboxylase subunit B gene (Pccb) in αKO cells (named p-αKO) leads to immune evasion, tumor progression and death of host mice. Surprisingly, p-αKO tumors are still infiltrated with T cells but they are inactive against tumor cells. However, blockade of PD-L1/PD1 interaction reactivated clonally expanded T cells infiltrating p-αKO tumors, leading slower tumor progression and improve survival of host mice. These results indicate that Pccb can modulate the activity of cytotoxic T cells infiltrating some pancreatic tumors and this understanding may help to improve immunotherapy for PDAC. aKO cells were generated by knocking out p110a from KPC, and Pccb was knocked out from aKO cells and generated p-aKO cells. Total RNA was extracted from the two cell lines (aKO vs p-aKO) and after polyA enrichment and library prep, samples were sequenced by illumina PE150.