Unravelling the mechanisms of acquired immunomodulatory drug resistance in multiple myeloma

Abstract

Immunomodulatory drugs (IMiDs) are a cornerstone of multiple myeloma treatment and newer cereblon E3 ligase modulating drugs (CELMoDs) are in clinical trials. However, a major barrier to improving patient outcomes is the inevitable development of resistance to these agents. IMiDs/CELMoDs bind to the cereblon (CRBN) component of the cullinA-RING E3 ubiquitin ligase and designate a new set of substrates for degradation via the proteasome. Generation of resistance is frequently associated with decreased CRBN expression, and this is associated with genetic alteration in ~1/3rd of patients. However, alternative drivers of the low CRBN state, and other mechanisms of resistance, need to be elucidated. My aim was to better understand the mechanisms driving acquired IMiD/CELMoD resistance and develop strategies to treat the resistant disease state. To tackle this complex problem, I generated and characterised myeloma cell line models with acquired IMiD/CELMoD resistance and performed multiomics analyses. The key findings of these analyses were then validated and explored further. Quantitative proteomics analysis identified common changes in lipid synthesis proteins across the resistant cell lines and glucose labelling experiments confirmed altered lipid flux. Proteomic analysis of paired patient samples, from diagnosis and relapse on IMiD, suggested similar changes in lipid pathways. A genome wide CRISPR screen performed in a cell line with acquired CELMoD resistance identified potential novel dependencies in the lipid pathway genes Stearoyl-CoA Desaturase (SCD) and Membrane Bound Transcription Factor Peptidase Site 1 (MBTPS1). This work has led to novel insights into lipid pathway changes in the IMiD/CELMoD-resistant state which may represent targetable vulnerabilities. Another novel dependency identified in the resistant lines was SET Domain Containing 2, Histone Lysine Methyltransferase (SETD2). SETD2 inhibition led to a greater reduction in proliferation in the IMiD/CELMoD-resistant cell lines compared to their sensitive control lines, and this was associated with a greater reduction in Neural Cell Adhesion Molecule 1 (NCAM1/CD56), Epithelial

Membrane Protein 2 (EMP2), and Thymosin Beta 15A (TMSB15A) expression, suggesting these genes may be key mediators of the effect. This work provides insights into the generation of IMiD/CELMoD resistance and identifies potential novel targeted treatment strategies for drug resistant myeloma.