Abstract 6831: Single-cell-based epigenetic and transcriptomic analysis in the KPC pancreatic cancer mouse model revealed dynamiccharacteristic subtypes of cancer-associated fibroblasts
Authors: Sasaki Keita , Shinjo Keiko , Wang Xingxing , Kumegawa Kohei , Raruyama Reo , Mii Shinji , Murofushi Yoshiteru , Suzuki Miho , Enomoto Atsushi , Kondo Yutaka 
Published: March 2024

Pancreatic cancer features robust fibrosis, with 40-80% fibrotic tissue and a dense stroma, highlighting the crucial need to grasp cellular interactions in the cancer microenvironment.

In this study, we used single-cell RNA sequencing (scRNA-seq) to analyze pancreatic tissues from 60-day-old normal mouse (n=1) (GSE125588) and KPC (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx-1-Cre) cancer model with tumor diameter of 1-2 cm (n=2) (GSE129455). By examining fibroblast clusters, we identified distinct subtypes of cancer-associated fibroblasts (CAFs), and revealed four clusters: normal fibroblasts cluster, inflammatory CAFs (iCAFs) cluster marked by increased expression of IL6 and other cytokines, myofibroblast CAFs (myCAFs) cluster solely in the KPC model, and antigen-presenting CAFs (apCAFs) cluster expressing Mesothelin. We found that expression pattern of iCAFs in the KPC appeared similar to normal cells than myCAFs, suggesting a potential role in inhibiting cancer. it is reported that mesothelial cells might transition to apCAFs under the influence of IL6 and TGFβ due to tissue damage and inflammatory effects. This transition was visualized in our apCAF cluster, suggesting a potential pathway for the transformation of mesothelial cells into apCAFs.

Next, in order to analyze epigenetic profiles of fibroblasts, we conducted single-cell Assay for Transposase-Accessible Chromatin with high-throughput sequencing (scATAC-seq) using 90-day-old KPC mice (n=2) and a wild-type mouse (n=1).scATAC-seq showed that there are mainly two clusters of fibroblasts, one cluster corresponded to myCAF, enriched with PDPN, while the other represented iCAF cluster, enriched with COL1A2. These data suggest that in terms of the epigenetic state, myCAF contain several different CAFs and have the potential to differentiate into either myCAFs or other type of based on certain stimulation. Ultimately, CAF differentiated into three distinct subtypes as revealed by scRNA-seq. This highlights that despite similar epigenetic states, various transcription factors characterize the functionality of these fibroblast subtypes. Further exploration of the underlying mechanism that lead to different CAF subtypes might help in controlling the microenvironment of pancreatic cancer.

Citation Format: Keita Sasaki, Keiko Shinjo, Xingxing Wang, Kohei Kumegawa, Reo Raruyama, Shinji Mii, Yoshiteru Murofushi, Miho Suzuki, Atsushi Enomoto, Yutaka Kondo. Single-cell-based epigenetic and transcriptomic analysis in the KPC pancreatic cancer mouse model revealed dynamiccharacteristic subtypes of cancer-associated fibroblasts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6831.