Targeting the lipid kinase PIKfyve in pancreatic ductal adenocarcinoma

ABSTRACT Pancreatic Ductal Adenocarcinoma (PDAC) subsists in a harsh, nutrient-disrupted microenvironment and thus upregulates autophagy and other lysosome-dependent nutrient recycling and acquisition processes. Unfortunately, progress in targeting these pathways has been hampered by the challenge of characterizing favorable targets for drug development. Our preliminary data suggests that PIKfyve is overexpressed in PDAC and that loss of PIKfyve decreases PDAC initiation and progression and increases survival in PDAC genetically engineered mouse models. Importantly, two PIKfyve inhibitors, ESK981 and apilimod, have both cleared phase 1 clinical trials. Further, ESK981 is currently being tested in a phase II clinical trial in patients with solid tumors including PDAC. Thus, PIKfyve may be a promising target for disrupting lysosome-dependent metabolic pathways in PDAC. Our long-term goal is to establish PIKfyve inhibition as a therapeutic strategy for PDAC. Our overall objective is to 1) dissect the role of PIKfyve in regulating metabolic homeostasis in PDAC and; 2) determine the mechanism and efficacy of the synergistic effects seen with dual PIKfyve and KRAS-MAPK inhibition in PDAC. The driving hypotheses are that PIKfyve maintain lipid homeostasis in PDAC through its regulation of autophagy and that inhibition of KRAS-MAPK perturbation sensitizes PDAC to PIKfyve inhibition through disrupting lipid homeostasis. Our preliminary data from a metabolism focused CRISPR knockout screen revealed that upon PIKfyve inhibition, de novo fatty acid synthesis genes FASN and ACACA became synthetically essential in PDAC. Additionally, RNA-sequencing analysis revealed that genes involved in lipid synthesis were significantly upregulated. We further demonstrated that inhibition of KRAS-MAPK, the ubiquitous driver oncogenic signaling pathway in PDAC, decreases transcription of FASN and ACACA. Finally, we showed that MEK (also known as MAPKK) inhibition synergistically suppressed PDAC growth in combination with PIKfyve inhibitor ESK981 in vitro in vivo. We plan to systematically extend upon these findings through the following Specific Aims. Aim 1 will focus on determining the mechanism through which PIKfyve regulates de novo lipid synthesis, particularly whether it is through the lysosome and or through the autophagic pathway. We will also determine whether this relationship translates to in vivo settings using xenograft and allograft models. Aim 2 will leverage novel mutant KRAS inhibitors that are in development pipelines to see whether they also synergize with PIKfyve inhibitors in vitro and in vivo. We will also assess dynamics of the synergistic effects between KRAS-MAPK inhibition and PIKfyve inhibition particularly focusing on whether this effect is due to the regulation of FASN and ACACA and or disruption of lipid homeostasis. Together, these aims will delineate a novel functional relationship between PIKfyve and lipid homeostasis in PDAC, establish a mechanistic rationale for dual targeting of KRAS-MAPK and PIKfyve in PDAC, and determine the efficacy of novel mutant KRAS inhibitors in combination with PIKfyve inhibitors as a rapidly translatable therapeutic strategy for PDAC.