Abstract Autophagy, a programmed self-eating process, underlies the progression of multifactorial diseases like pancreatic ductal adenocarcinoma (PDA). Although autophagy can be regulated by nutrients availability, the contribution of other key environmental factors is not well-understood. Fibrosis is a key characteristic of PDA, where the abundance of extracellular matrix (ECM) components, such as laminins and collagens, predicts poorer survival in patients. Although the remodeling of the ECM has been shown to be crucial for PDA tumorigenesis, its impact on vital processes for PDA such as autophagy is still largely unexplored. Through combining functional genomics and tumor-like 3D cultures, we discovered that PDA cells regulate their autophagy levels by sensing the ECM through the integrinα3-Hippo-YAP1 axis. Mechanistically, integrinα3 inhibits the upstream Hippo pathway (e. g. NF2 and LATS1/2) to activate YAP1, which in turn cooperates with co-repressive factors (e. g. NCOR1, HDAC3) to finetune the expression of a large network of autophagy/lysosome genes and control autophagy flux levels. Single-cell RNA-Seq (scRNA-Seq) analysis on PDA patients’ tumors confirmed the inverse relationship between YAP1 activity and autophagy flux levels. Namely, PDA cells with the highest expression of YAP1-conserved genes, displayed the lowest expression of autophagy/lysosome genes and vice versa. In mouse models, the spatial proximity of PDA cells to the key ECM component, laminin, shaped their intracellular autophagy levels and biological responses. Namely, PDA cells actively sensing laminin displayed low-autophagy levels and were conducive to growth. On the other hand, PDA cells with reduced laminin sensing exhibited high-autophagy levels and were tolerant to chemotherapy. The scRNA-Seq on PDA patients’ tumors confirmed the presence of autophagic heterogeneity at the transcriptional level in PDA cells. Additionally, our transcriptomics on patient samples validated the proliferative and chemo-tolerant potentials of the low-autophagy and high-autophagy PDA populations, respectively. Targeting the ECM-mediated autophagy regulation reduced autophagic heterogeneity, altered PDA growth and shaped antitumor responses to FDA-approved therapies. Namely, targeting integrinα3 synergized with chloroquine and chemotherapy to promote stabilization and/or regression of PDA xenografts. In summary, we reveal a non-metabolic regulation of autophagy through ECM sensing, opening the possibility to investigate and target ECM-specific outputs in various contexts including PDA, acquired therapeutic resistance and other fibrotic and developmental disorders. Citation Format: Mohamad Assi, Ruohong Wang, Emily A. Kawaler, Albert SW. Sohn, Zahid Dewan, Joel Encarnacion-Rosado, Kevin S. Kapner, Koelina Ganguly, Joao Paulo, Diane Simeone, Andrew Aguirre, Robert S. Banh, Alec C. Kimmelman. Extracellular matrix sensing shapes the heterogeneity of autophagic flux and biological responses in pancreatic cancer 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 (18Suppl₃): Abstract nr A022.
Assi et al. (Sun,) studied this question.