Abstract B107: FOXA1/2 and HNF4α Regulate Molecular Subtype and Therapeutic Response in Pancreatic Ductal Adenocarcinoma

Abstract Cell identity, tightly regulated by transcription factors (TFs), is frequently disrupted in cancer, driving tumor progression and metastasis. In pancreatic ductal adenocarcinoma (PDAC), alterations in cell identity contribute to disease heterogeneity and therapy resistance. Integrated genomic, transcriptomic, and proteomic analyses have defined two major PDAC subtypes: classical and basal. Notably, recent evidence suggests that changes in subtype identity can enable resistance to targeted therapies. These subtypes are distinguished by relative levels of endodermal lineage-specifying TFs such as FOXA1/2 and HNF4α, which are maintained in the classical subtype but downregulated in the basal subtype. Understanding how these TFs shape cellular identity is critical for identifying therapeutic vulnerabilities and mechanisms of drug resistance. We have shown that HNF4⍺ promotes the classical subtype program of PDAC. Although FOXA1/2 and HNF4α regulate gene expression in normal tissues, it is still unclear whether such cooperation is necessary to drive the classical transcriptional program in PDAC. We hypothesize that FOXA1/2 and HNF4α cooperatively regulates the gene expression program that regulates the classical subtype program in PDAC. Using human cell lines and murine PDAC organoid models, we reconstituted and modulated TF expression to evaluate downstream gene expression and TF genomic binding via ChIP-seq. Conditional alleles of FoxA1/2 in our murine organoid lines reveal that loss of FOXA1/2 lead to a decrease in the classical program. When we overexpress HNF4α in FOXA1/2-null organoids, it leads to a decrease in organoid growth; therefore, illustrating the ability of HNF4α to regulate growth independent of FOXA1/2. In a human cell line, we find that co-expression of FOXA1/2 and HNF4a activates the classical B signature while FoxA2 alone activates the Classical A signature, indicating that FOXA2 and HNF4a activate subtype-specific transcriptional programs. Additionally, we demonstrate that the overexpression of HNF4a in a subcutaneous xenograft model confers resistance to KRASG12C inhibition, leading to an increase in tumor size and weight. Unexpectedly, we find that these TFs do not cooperatively regulate gene expression; rather, in the human cell line, FOXA2 interferes with HNF4α genomic binding, suggesting a competitive or inhibitory interaction. Overall, our work highlights how lineage-defining TFs govern PDAC cell identity and therapeutic response. Citation Format: Walter A. Orellana, Sydney N. Larsen, Eric L. Snyder. FOXA1/2 and HNF4α Regulate Molecular Subtype and Therapeutic Response in Pancreatic Ductal Adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research—Emerging Science Driving Transformative Solutions; Boston, MA; 2025 Sep 28-Oct 1; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_3):Abstract nr B107.