CRISPR screen of human pancreatic cancer xenografts identifies a KLF5 proliferation vulnerability through epigenetic modifiers NCAPD2 and MTHFD1

One of the major conundrums of cancer research and treatment is that the metastases that lead to death in most patients do not appear to involve additional driver mutations. Previously, we reported widespread loss of heterochromatin with activation of pro-metastatic genes in the subset of cells of primary pancreatic tumors that gave rise to liver and lung metastases. Here we hypothesized that this change in chromatin could create unique vulnerabilities in distant metastases. Using a CRISPR screen of human patient-derived xenografts from metastases and primary tumors, we identified KLF5 as essential for metastatic cell proliferation but not primary tumor growth. Further, we found that KLF5 induced epigenetic modifier genes, including NCAPD2 and MTHFD1, which themselves facilitated expression of specific genes driving migration and epithelial-mesenchymal transition, including TGFBR2, VIM, EMP1, and ITGB1. Inhibition of expression of these modifier genes restored heterochromatin in the specific regions that distinguish the primary and metastatic tumors. We backed up this causal chain of evidence with rigorous additional knockdown experiments with the modifier genes, and single cell RNA and chromatin experiments, and we also replicated the main findings in a second set of paired primary and distant metastasis xenograft lines. Finally, KLF5 expression was strongly associated with patient survival and human PDAC cell plasticity in a dataset of 70 PDAC patients and KLF5 expression was increased in the majority of lung, liver and peritoneal metastases compared to the matched primary tumor, confirming its importance in PDAC metastasis and mortality. In summary, we have identified a cascade of epigenetic modulators, modifiers and mediators that maintains the widespread heterochromatin loss supporting metastatic cell proliferation in human pancreatic cancer (see Graphical Abstract).