P-179: Altered Lipid Metabolism in IMiD/CELMoD Resistant Multiple Myeloma Confers Novel and Targetable Vulnerabilities

Introduction: IMiDs/CELMoDs are a cornerstone of myeloma treatment; however a major barrier to improving patient outcomes is the inevitable development of drug resistance. Understanding resistance mechanisms is critical to enable the advancement of targeted treatment strategies.

Methods: Acquired IMiD/CELMoD resistant MM1s and H929 myeloma cell lines were characterised by whole exome sequencing, RNA-seq and proteomics. A genome-wide loss-of-function CRISPR screen was carried out in Iberdomide (Iber)-resistant MM1s; gene effect scores were calculated with the Chronos model and compared to parental MM1s using data from the DepMap portal. Membrane Bound Transcription Factor Peptidase Site 1 (MBTPS1) inhibitor PF-429242 was used to inhibit activation of the Sterol Regulatory-Element Binding Protein (SREBP) pathway. Stable isotope labelling experiments using 13C6-glucose assessed lipid synthesis. Using unpaired patient RNA-seq data, lipid gene transcript levels were compared between 736 newly diagnosed patients and 270 patients relapsing on lenalidomide.

Results: Quantitative proteomic analysis identified common changes in lipid synthesis pathways, including the SREBP pathway, across the resistant cell lines. Stearoyl-CoA Desaturase (SCD), a key effector of the SREBP pathway, was one of only 5 proteins with significantly altered expression in all 6 resistant lines compared to control (log2FCs ranging from -0.37 to -1.50 (adj p < 0.05)).
A genome-wide CRISPR screen using Iber-resistant MM1s cells identified potential new dependencies (gene effect score <-1 in resistant cells and >-0.5 in parental cells) in 47 genes including SCD and MBTPS1. MBTPS1 is critical for activation of the SREBP pathway and demonstrated one of the largest changes in gene effect (-1.4 vs –0.3). PF-429242 showed significantly greater reduction in cell proliferation in the IMiD/CELMoD resistant H929 cells compared to controls.
13C6-glucose labelling experiments showed that in Iber-resistant MM1s and H929 (compared to controls) the proportion of newly synthesised palmitic and stearic acid was reduced. The oleic acid/stearic acid and palmitoleic acid/palmitic acid ratios were also decreased, suggesting the flux of fatty acid desaturation catalysed by SCD was reduced. The fraction of glucose-derived lipogenic acetyl-CoA was also reduced in the resistant lines, indicating that resistance decreased glucose contribution to fatty acid synthesis with potential use of alternative carbon sources. There was a trend for increased synthesis of saturated fatty acids with PF-429242 treatment in Iber-resistant H929, but not its control.
In patient RNA-seq data several fatty acid synthesis genes were significantly differentially expressed, including SCD and MBTPS1, suggesting the changes seen in cell lines may be replicated in patient data.

Conclusions: The development of IMiD/CELMoD resistance is associated with alterations in lipid metabolism, suggesting a role in resistance biology that may confer novel and targetable vulnerabilities.