Targeting HNF1A-mediated therapeutic resistance in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDA) is one of the deadliest cancers with a survival rate of 11% due to its
aggressive nature and resistance to therapies. While nearly all PDA cases are driven by mutations in the
KRAS gene, efforts to target KRAS or its effectors (e.g., MEK and ERK) are met with adaptive resistance.
Pancreatic cancer stem cells (PCSCs), a subpopulation of transcriptionally-plastic cancer cells that are
especially drug resistant and particularly tumorigenic, are a critical component of the aggressive and therapy-
resistant nature of PDA. There are currently no strategies to target PCSCs, as well as a lack of information
regarding their drivers. We previously identified HNF1A, a gastrointestinal-lineage transcription factor, as a
novel master regulator of the PCSC state. Our preliminary data show that HNF1A expression can be potently
blocked by BET-inhibitors (BETi), a class of drugs which inhibit the epigenetic reader protein BRD4.
Interestingly, re-expression of HNF1A rescues cell cycle progression and PCSC-properties in BETi-treated
PDA cells, suggesting that HNF1A is a novel and critical target for these drugs. We have also found that
HNF1A is a novel driver of resistance to targeting KRAS and downstream MEK/ERK-signaling. Importantly, the
use of BETi in combination with MEK- and ERK-inhibitors (MEKi/ERKi) increases growth arrest and cell death
in an HNF1A-dependent manner. We hypothesize that HNF1A is directly regulated by BRD4, and is therefore
targetable with BETi, and that the inhibition of HNF1A expression with BETi will nullify HNF1A-dependent
PCSCs and adaptive resistance to KRAS-ablation. In this proposal, we aim to characterize the regulation of
HNF1A and its role in therapeutic response and resistance. In Specific Aim 1, we will characterize the
regulation of HNF1A by BETi-target BRD4. Specific Aim 1 will combine genetic manipulation of BRD4, ChIP-
PCR, and reporter assays to demonstrate regulation of HNF1A by BRD4. Re-expression of HNF1A in BRD4-
depleted cells will 1) define the role of HNF1A in BRD4-mediated cell growth and survival in vitro and in vivo,
as well as 2) determine the contribution of HNF1A to the BRD4 transcriptome using RNA-seq/ChIP-seq to
identify how HNF1A determines response to BETi. In Specific Aim 2, we will establish BETi as a means to
overcome HNF1A-mediated resistance to KRAS-ablation. Specific Aim 2 will use PDA cells with and without
ectopic HNF1A expression to examine the contribution of HNF1A to BETi and KRAS-pathway inhibitor activity;
we will utilize in vitro and in vivo assays to examine how these drugs affect PCSCs and use RNA-seq/ChIP-
seq to determine how HNF1A promotes resistance to targeting KRAS-signaling. Both aims will utilize next-
generation bromodomain-selective inhibitors that have not been explored in PDA or combinatorial therapies.
The completion of the above studies will dramatically improve our understanding of PDA biology and uncover
novel therapeutic targets. By improving our understanding of resistance to KRAS suppression and expanding
the therapeutic spectrum of PDA to include PCSCs, more effective treatment of PDA can be achieved.

Grant Number: 5R37CA275961-04
NIH Institute/Center: NIH
Principal Investigator: Ethan Abel