Autophagy/lysosome disruption via pikfyve inhibition in multiple myeloma

Abstract We previously reported achemo-genomics screen that unexpectedly identified phosphatidylinositol-3-phosphate 5 kinase (PIKfyve) as a vulnerable target in multiple myeloma (MM). PIKfyve regulates lysosomal function and autophagy, a catabolic process critical for recycling cellular components, plasma cell homeostasis, and sustained immunoglobulin synthesis. Given the high basal requirements of autophagy in MM, targeting autophagy holds potential as a novel therapeutic avenue. Here, we describe the development and characterization of novel, selective and potent small-molecule PIKfyve inhibitors. The most studied of these, PIK001, showed robust single agent anti-MM activity in vitro, synergized with established anti-MM agents (including immunomodulatory drugs, proteasome inhibitors, venetoclax, and selinexor), and retained efficacy in lenalidomide-resistant models. Ex vivo activity of PIK001 was also demonstrated through single cell gene expression analysis in six primary patient samples, with all samples showing upregulated gene expression of apoptosis-related genes. With further iteration we developed a next-generation compound with superior potency and improved pharmacokinetic properties (PIK085). As expected, PIKfyve inhibition impaired autophagic flux, evidenced by a doubling of Sequestosome-1 expression, an adaptor for the selective autophagy of ubiquitinated proteins, as well as upregulation of lysosomal genes in vitro and ex vivo. PIK001 also induced the classical cellular vacuolation phenotype widely associated with disruption of PIKfyve activity due to its role in vacuole maturation. Multi-omic profiling of three isogenic human myeloma cell line (HMCL) pairs sensitive / resistant to PIK001 revealed distinct resistance mechanisms: a clonal PIKfyve catalytic domain mutation (PIKFYVEN1939K) in KMS26 PIK001-resistant, and PIKfyve protein overexpression in JJN3 and KMS11 PIK001-resistant HMCLs. Unbiased proteomics identified ~7,000 unique proteins per isogenic HMCL pair, with resistant cells showing enrichment of lysosomal and apoptosis-related proteins and striking upregulation of proteins involved in antigen processing and MHC complex presentation in KMS11 PIK001-resistant. Given this observation, we next demonstrated that treatment of sensitive HMCLs with PIK001 (50 nM, 72h) significantly increased cell-surface MHC Class I protein expression in HMCLs sensitive to PIKfyve inhibition. Likewise, exposure to PIK001 also resulted in a marked increase in MHC Class I gene expression at the single cell level in 4/6 primary MM patient samples. The MHC upregulation suggests that PIKfyve inhibition may enhance tumor immunogenicity. Surprisingly, the most enriched signaling pathway following PIK001 exposure in vitro was the MSigDB Hallmark Cholesterol Homeostasis pathway, with total cholesterol levels increased in all three HMCLs following PIKfyve inhibition. Notably, PIK001 combined with the HMG-CoA reductase inhibitor fluvastatin resulted in antagonistic effects,highlighting the functional relevance of cholesterol metabolism in PIKfyve inhibitor-induced cytotoxicity. Upregulation of cholesterol biosynthesis genes following PIK001 exposure was also demonstrated ex vivo. Our findings establish PIKfyve inhibition as a compelling target in MM, elucidates distinct mechanisms of resistance, and reveal unexpected links to cholesterol metabolism and tumor immunity as a consequence of autophagy disruption in MM—laying a strong preclinical foundation for further mechanistic studies and therapeutic development.