Abstract 4158: PIKfyve inhibition drives lipogenic adaptation and reveals metabolic vulnerabilities in PDAC
Authors: Ruya Pakkan, Caleb Cheng, Jasmine Wisniewski, Sydney Peters, Pietro Morlacchi, Li Zhang, Yuanyuan Qiao, Costas A. Lyssiotis, Arul M. Chinnaiyan
Journal: Cancer Research (2025)

Abstract PIKfyve plays a key role in autophagy and lysosomal functions, which are critical for pancreatic ductal adenocarcinoma (PDAC) cell metabolism and survival. Consistent with this, we found that PIKfyve perturbation suppresses autophagy and reduces PDAC cell viability. Prior studies show that autophagy and lysosomal processes are critical for maintaining iron homeostasis and mitochondrial respiration in PDAC. However, PIKfyve inhibition did not seem to significantly affect oxygen consumption rate (OCR) compared to other lysosomal inhibitors such as chloroquine and bafilomycin, suggesting that PIKfyve also regulates other metabolic demands in addition to iron homeostasis. To understand the role of PIKfyve in PDAC and detect genes essential for metabolic compensation to PIKfyve loss, we performed a CRISPR screen using the PIKfyve inhibitor apilimod as a selective pressure. This revealed that the most depleted sgRNAs targeted genes involved in de novo fatty acid synthesis, insinuating that de novo fatty acid synthesis acts as a functional adaption to loss of PIKfyve function. Consistent with these results, cells upon disruption of fatty acid synthesis were sensitized to PIKfyve inhibitors, confirming that PIKfyve perturbation makes cells more reliant on fatty acid synthesis for survival. Moreover, PIKfyve inhibition activated key lipogenic transcriptional factor SREBP1 and upregulated fatty acid synthesis genes such as FASN and ACACA. We further discovered that PIKfyve inhibition in PDAC cells changed cellular metabolism, with initial decreases in citrate levels and subsequent recovery, along with a decrease in upstream glycolytic metabolites. Targeted lipidomics and isotope tracing showed that PIKfyve inhibition rerouted glucose-derived carbon into de novo lipid synthesis, specifically sphingolipids, dependent on SREBP1 activity. An additional CRISPR screen using a more potent degree of PIKfyve inhibition further identified sphingolipid synthesis genes (SPTLC1, SPTLC2, and KDSR) as essential for cell survival under PIKfyve inhibition. These results suggest that PIKfyve inhibition drives an adaptive increase in lipid synthesis, specifically sphingolipid synthesis through the activation of SREBP1 as a survival mechanism for PDAC cells. These results show a metabolic vulnerability in PDAC, suggesting that PIKfyve inhibitors, in combination with the inhibition of fatty acid synthesis and specifically sphingolipid synthesis, represent promising therapeutic strategies. Citation Format: Ruya Pakkan, Caleb Cheng, Jasmine Wisniewski‬‬, Sydney Peters, Pietro Morlacchi, Li Zhang, Yuanyuan Qiao, Costas A. Lyssiotis‬‬, Arul M. Chinnaiyan‬. PIKfyve inhibition drives lipogenic adaptation and reveals metabolic vulnerabilities in PDAC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4158.‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬