Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by a poor prognosis, and resistance to gemcitabine, a frontline chemotherapeutic agent, poses a significant challenge to effective treatment. Unraveling the molecular underpinnings of gemcitabine resistance is essential for devising novel therapeutic strategies. Here we derived gemcitabine-resistant and parental pancreatic cancer cell lines from KPC mouse models of PDAC. Employing a multi-omics approach, we integrated RNA-seq, ATAC-seq, and ChIP-seq analyses to characterize the genome-wide alterations in gene transcription, chromatin accessibility, histone modifications, and transcription factor (TF) binding in resistant cells. High-throughput chromatin conformation capture (Hi-C) was used to explore 3D chromatin remodeling. Our analyses identified differentially expressed genes (DEGs) critical for gemcitabine metabolism and resistance, notably Rrm1 and Cdadc1. We observed the upregulation of NF-kB, p53, and MAPK pathways, and the downregulation of mTORC1, MYC targets, and reactive oxygen species pathways. Differentially accessible regions (DARs) showed a significant positive correlation with the expression patterns of DEGs and histone mark H3K27 acetylation. Motif enrichment analyses revealed that TFs from the AP-1, Fox, and Hox families were significantly enriched at DARs, underscoring Foxa1 as a pivotal regulator of resistance-associated genes. We discovered that 3D chromatin reorganization, particularly the enhancement of enhancer-promoter interactions involving super-enhancer (SE) reprogramming mediated by Foxa1 and Ctcf/Smc3, drives the expression of critical resistance genes. Targeting Foxa1 or disrupting SE-associated transcription using JQ1, a bromodomain inhibitor, effectively inhibited resistant cell proliferation and enhanced gemcitabine sensitivity. In summary, this study elucidates the role of TF-mediated chromatin remodeling in gemcitabine resistance and suggests that targeting super-enhancers could be a promising therapeutic strategy to overcome resistance in PDAC, potentially revolutionizing drug therapy for this disease.