Dissection of transcriptional and cis ‐regulatory control of differentiation in human pancreatic cancer

Abstract

The histological grade of carcinomas describes the ability of tumor cells to organize in differentiated epithelial structures and has prognostic and therapeutic impact. Here, we show that differential usage of the genomic repertoire of transcriptional enhancers leads to grade-specific gene expression programs in human pancreatic ductal adenocarcinoma (PDAC). By integrating gene expression profiling, epigenomic footprinting, and loss-of-function experiments in PDAC cell lines of different grade, we identified the repertoires of enhancers specific to high-and low-grade PDACs and the cognate set of transcription factors acting to maintain their activity. Among the candidate regulators of PDAC differentiation, KLF5 was selectively expressed in pre-neoplastic lesions and low-grade primary PDACs and cell lines, where it maintained the acetylation of grade-specific enhancers, the expression of epithelial genes such as keratins and mucins, and the ability to organize glandular epithelia in xenografts. The identification of the transcription factors controlling differentiation in PDACs will help clarify the molecular bases of its heterogeneity and progression.

Enhancer Reprogramming Promotes Pancreatic Cancer Metastasis

“…We confirmed this overall pattern of FOXA1 upregulation by RT-qPCR analysis of human PDA organoids and by immunohistochemical staining of PDA tissue derived from a rapid autopsy program (Figure S3E–G). In addition, levels of FOXA1 expression were correlated with the degree of GAIN enhancer activation in human PDA cell lines (Figure S2J) (Diaferia et al, 2016). These results validate that FOXA1 upregulation occurs during human PDA progression.…”

“…Prior studies have associated low FOXA1 expression with the acquisition of mesenchymal features in PDA cell lines (Diaferia et al, 2016; Song et al, 2010). However, no study to date has evaluated the functional consequences of FOXA1 upregulation in PDA.…”

“…using the Assay for Transposase-Accessible Chromatin [ATAC-seq]) allow for the annotation of active enhancer landscapes in different cellular states (Yue et al, 2014). One study has applied ChIP-seq analysis to human PDA cell lines to expose enhancer profiles and TFs that correlate with the degree of epithelial differentiation, or disease ‘grade’ (Diaferia et al, 2016). However, it has yet to be determined how the enhancer landscape evolves during each stage of PDA progression.…”

ZEB1‐regulated inflammatory phenotype in breast cancer cells

“…Our data were then compared to all of the publically available human ZEB1‐binding data for human pancreatic carcinoma Panc‐1, human hepatoblastoma HepG2, and the Gm12878 B‐lymphoblastic cell lines using the same read aligner, peak caller, and parameters (Diaferia et al ., 2016; Hensen et al ., 2014). We found that MDA‐231‐D cells and HepG2 cells had distinct profiles in terms of their ZEB1‐binding regions and that Hs578T and Panc‐1 cells, but not Gm12878 cells, shared ZEB1‐binding regions with MDA‐231‐D cells (Fig.…”

“…It was recently reported that the EMT is involved in cancer malignancy by contributing not only to metastasis but also to the acquisition of cancer stem cell properties and chemoresistance (Fischer et al ., 2015; Ye and Weinberg, 2015; Ye et al ., 2015; Zheng et al ., 2015). A recent genome‐wide analysis of EMT‐related transcription factor binding regions in pancreatic cancer cells suggested that ZEB1 plays a role in inducing the mesenchymal phenotype by suppressing enhancers that regulate the expression of epithelial genes (Diaferia et al ., 2016). However, that analysis focused only on epithelial gene expression that was related to the EMT.…”