Abstract A107: Multi-Omic Single-cell Sequencing Reveals KMT2D Loss Activates AP-1-Driven Enhancer Reprogramming to Promote Epithelial-to-Mesenchymal Plasticity in Pancreatic Cancer
Raghunath Ranga Sudharshan, Hong Sun. Kim, Heizel Acosta, Shungang Zhang, Marina Pasca di Magliano, Arvind Rao, Jiaqi ShiAbstract
Background:
KMT2D, a histone H3K4 methyltransferase and critical epigenetic regulator, is mutated in approximately 11% of pancreatic ductal adenocarcinoma (PDAC) cases. Prior work from our group demonstrated that KMT2D loss drives epithelial-to-mesenchymal plasticity (EMP) and tumor progression in PDAC; however, the downstream transcriptional mechanisms remain poorly defined. Here, we investigated how KMT2D loss rewires enhancer accessibility and transcription factor (TF) networks to promote EMP in PDAC.
Methods:
A pancreas-specific Mll4 (mouse KMT2D gene) knockout mouse model (KPCM: KrasG12D/+; Trp53R172H/+; Ptf1a-Cre; Mll4SETflox/flox) was generated alongside KPC (KrasG12D/+; Trp53R172H/+; Ptf1a-Cre) controls to assess the impact of KMT2D on tumor progression in vivo. Single-nucleus ATAC-seq (snATAC-seq) and single-cell RNA-seq (scRNA-seq) were performed on both models, with all downstream analyses focused on pancreatic epithelial cells. Differential chromatin accessibility analysis was performed in enhancer regions defined by the ENCODE project, followed by TF motif enrichment and footprinting to identify candidate regulators. ChromVAR was used to quantify genome-wide motif deviation scores in epithelial cells. Peak-to-gene linkage mapping connected accessible enhancers to downstream transcriptional targets, and pathway enrichment was performed on KPCM-upregulated linked genes. Pseudotime trajectories from acinar-to-ductal states were reconstructed, and per-feature differential slopes (KPCM - KPC) were computed for both motif deviation scores and gene expression across ordered trajectory bins.
Results:
Differential enhancer accessibility analysis of snATAC-seq data in KPCM epithelial cells identified AP-1 family motifs as consistently top-ranked, with footprinting confirming significantly increased AP-1 occupancy in KPCM compared with KPC pancreatic epithelial cells. ChromVAR deviation scores for AP-1 motifs were considerably more positive in KPCM pancreatic epithelial cells compared with KPC, indicating genome-wide enhancer activation. Peak-to-gene linkage mapping revealed that AP-1-associated motifs in KPCM pancreatic epithelial cells are linked to upregulated downstream genes enriched in EMP-associated pathways. Pseudotime analysis concordant positive differential trends in both motif deviation and gene expression across the trajectory in KPCM, with AP-1 family members emerging as the most consistently enriched TFs.
Conclusion:
Integrative multi-omic single-cell sequencing analysis of pancreatic epithelial cells identifies AP-1 family activation as a candidate effector of KMT2D loss in PDAC. Convergent chromatin accessibility and transcriptional analyses demonstrate enhanced AP-1 pathway activity in KMT2D-deficient pancreatic epithelial cells. This activation drives expression of downstream epithelial-mesenchymal plasticity (EMP) regulators, including Itgb4 and Sox4. These findings identify an important mechanism underlying the tumor suppressive role of KMT2D in PDAC.
Citation Format:
Raghunath Ranga Sudharshan, Hong Sun. Kim, Heizel Acosta, Shungang Zhang, Marina Pasca di Magliano, Arvind Rao, Jiaqi Shi. Multi-Omic Single-cell Sequencing Reveals KMT2D Loss Activates AP-1-Driven Enhancer Reprogramming to Promote Epithelial-to-Mesenchymal Plasticity in Pancreatic Cancer [abstract]. In: Proceedings of the AACR Conference on Pancreatic Cancer: New Frontiers in Biology and Therapeutic Development; 2026 Sep 25-28; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(18_Suppl_2):Abstract nr A107.