TP63-Mediated Enhancer Reprogramming Drives the Squamous Subtype of Pancreatic Ductal Adenocarcinoma

Abstract

SUMMARY The aberrant expression of squamous lineage markers in pancreatic ductal adenocarcinoma (PDA) has been correlated with poor clinical outcomes. However, the functional role of this putative transdifferentiation event in PDA pathogenesis remains unclear. Here, we show that expression of the transcription factor TP63 (∆Np63) is sufficient to install and sustain the enhancer landscape and transcriptional signature of the squamous lineage in human PDA cells. We also demonstrate that TP63-driven enhancer reprogramming promotes aggressive tumor phenotypes, including enhanced cell motility and invasion, and an accelerated growth of primary PDA tumors and metastases in vivo. This process ultimately leads to a powerful addiction of squamous PDA cells to continuous TP63 expression. Our study demonstrates the functional significance of squamous transdifferentiation in PDA and reveals TP63-based reprogramming as an experimental tool for investigating mechanisms and vulnerabilities linked to this aberrant cell fate transition.

Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation

“…Notably, KLM1 is the only TP63-postive PDA cell line we have identified which does not exhibit a growth arrest phenotype in vitro following TP63 inactivation ( Fig. S2G-H) (Somerville et al, 2018). Importantly, KLM1 cells harbor a similar transcriptional and epigenomic profile as observed in other TP63-expressing PDA cell lines ( Fig.…”

“…S100A2, KRT5) ( Fig. 3D, S3L and Table S3) Somerville et al, 2018). Within the mouse stromal compartment, we identified 500 genes that were significantly upregulated in SUIT2-TP63 tumors compared to controls ( Fig.…”

“…In a prior study, we found that ectopic expression of TP63 in the human PDA cell line SUIT2 (which lacks endogenous TP63 expression) enhanced cell growth when implanted into the mouse pancreas in vivo, yet this phenotype was absent under tissue culture conditions (Somerville et al, 2018). These findings led us to hypothesize that TP63 expression alters how PDA cells communicate with non-neoplastic cells in the tumor stroma.…”

“…Of note, MIAPaca2 cells only express the TA isoform of TP63 ( Fig. S1A) and lack expression of squamous lineage markers (Somerville et al, 2018) and in fact are more representative of a cell type of neuroendocrine origin (Yu et al, 2019). The collected media was then applied to quiescent murine pancreatic stellate cells (PSCs), which are a precursor of CAFs in PDA, and RNA-sequencing analysis was performed on the PSC cultures following 96 hours to evaluate the cellular response ( Fig.…”

“…We next evaluated the relevance of the TP63-induced secretory phenotype in an in vivo model of PDA. For this purpose, we first infected SUIT2-luciferase cells (Somerville et al, 2018) with a TP63 cDNA or empty vector prior to orthotopic transplantation into the pancreas of NOD-scid gamma (NSG) mice. In accordance with our previous findings (Somerville et al, 2018), TP63 expression enhanced the growth of SUIT2 cells in vivo, but not in vitro ( Fig.…”