Reciprocal regulation of pancreatic ductal adenocarcinoma growth and molecular subtype by HNF4α and SIX1/4

Abstract

ObjectivePancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with a 5-year survival of less than 5%. Transcriptomic analysis has identified two clinically relevant molecular subtypes of PDAC: classical and basal-like. The classical subtype is characterised by a more favourable prognosis and better response to chemotherapy than the basal-like subtype. The classical subtype also expresses higher levels of lineage specifiers that regulate endodermal differentiation, including the nuclear receptor hepatocyte nuclear factor 4 α (HNF4α). The objective of this study is to evaluate the role of HNF4α, SIX4 and SIX1 in regulating the growth and molecular subtype of PDAC.DesignWe manipulate the expression of HNF4α, SIX4 and SIX1 in multiple in vitro and in vivo PDAC models. We determine the consequences of manipulating these genes on PDAC growth, differentiation and molecular subtype using functional assays, gene expression analysis and cross-species comparisons with human datasets.ResultsWe show that HNF4α restrains tumour growth and drives tumour cells toward an epithelial identity. Gene expression analysis of murine models and human tumours shows that HNF4α activates expression of genes associated with the classical subtype. HNF4α also directly represses SIX4 and SIX1, two mesodermal/neuronal lineage specifiers expressed in the basal-like subtype. Finally, SIX4 and SIX1 drive proliferation and regulate differentiation in HNF4α-negative PDAC.ConclusionOur data show that HNF4α regulates the growth and molecular subtype of PDAC by multiple mechanisms, including activation of the classical gene expression programme and repression of SIX4 and SIX1, which may represent novel dependencies of the basal-like subtype.

Single-nucleus and spatial transcriptomics of archival pancreatic cancer reveals multi-compartment reprogramming after neoadjuvant treatment

“…More generally, these programs may reflect a shift towards either basal-like or terminallydifferentiated pancreatic cell states that are advantageous for surviving CRT compared to a less differentiated classical-like phenotype (Figure 3D). This model is consistent with in vitro and in vivo evidence for lineage plasticity in normal pancreatic ductal progenitor cells (102) and differentiated pancreatic cells-including a role for MYT1/MYT1L, a member of the classical neuroendocrine-like program, in ductal-neuroendocrine reprogramming (Figure 3B; Tables S3-4) (103)(104)(105)(106)(107)(108).…”

“…Identifying cancer cell-and fibroblast-intrinsic programs that may govern local immune microniches remains an open question in PDAC research, with prior studies disagreeing on whether the basal-like or classicallike subtype is correlated with immune exclusion (11,89,90). Moreover, elucidating the relationships between our newly-identified neoplastic, lineage-specific programs (81,(102)(103)(104)(105)(106)(107)(108) and local immune infiltration will be critical in guiding therapeutic development.…”

A GATA6-centred gene regulatory network involving HNFs and ΔNp63 controls plasticity and immune escape in pancreatic cancer

“…1 27-30 HNF4A, in particular, was recently shown to support the classical phenotype by repressing the basal-related genes SIX1 and SIX4, among others. 31 However, Hnf4a deletion in mouse PDAC organoids was not enough to induce the full basal phenotype, suggesting that GATA6 and HNF4A have overlapping but not identical roles in maintaining lineage identity 31 and that GATA6 has a stronger antibasal function. Consistently, GATA6 loss in patient-derived samples was always broader and more pronounced than HNF4A loss, supporting a chronological hierarchy during PDAC progression towards basality (figure 2E).…”

Deregulation of Transcription Factor Networks Driving Cell Plasticity and Metastasis in Pancreatic Cancer

“…Apart from repressing FOXA1 , BACH1 activates SNAI2, which further promotes EMT, assessed by gene inactivation in human cell lines ( Sato et al, 2020 ). Transcriptomic analysis on primary tumors and patient-derived cell lines revealed that during tumorigenesis HNF4α directly activates HNF1A , and loss of the former enables a transition towards a more squamous phenotype ( Brunton et al, 2020 ; Camolotto et al, 2021 ). Moreover, HNF4α directly represses the mesodermal and neural differentiation TFs SIX1/4 , whose elevated expression was linked to the squamous subtype ( Camolotto et al, 2021 ).…”

“…Transcriptomic analysis on primary tumors and patient-derived cell lines revealed that during tumorigenesis HNF4α directly activates HNF1A , and loss of the former enables a transition towards a more squamous phenotype ( Brunton et al, 2020 ; Camolotto et al, 2021 ). Moreover, HNF4α directly represses the mesodermal and neural differentiation TFs SIX1/4 , whose elevated expression was linked to the squamous subtype ( Camolotto et al, 2021 ). Downregulation of HNF1A is observed in the tumor vs. normal pancreas, suggesting that decreased HNF1α levels are important for PDAC tumor progression ( Hoskins et al, 2014 ; Luo et al, 2015 ).…”