Abstract 3079: Uncovering novel molecular mechanisms of PI resistance in multiple myeloma through multi-omics analysis
Authors: Seungbin Han, Chien-Yun Lee, Lenka Besse, Umair Munawar, Shilpa Kurian, Andrej Besse, Ann-Sohpie Hainold, Silvia Nerreter, Cornelia Vogt, Johanna Thurner, Nina Rein, Max Köppel, Xiang Zhou, Larissa Haertle, Christoph Driessen, Hermann Einsele, Leo Rasche, Ondrej Slaby, Johannes Waldschmidt, Bernhard Küster, Klaus Martin Kortüm
Journal: Cancer Research (2025)

Abstract Background: Even with considerable advancements in multiple myeloma (MM) therapy, proteasome inhibitors (PIs) continue to be an indispensable treatment pillar in MM. However, the development of PI resistance remains a significant clinical challenge. Previous studies proposed different causes contributing to PI-resistance, though, these mechanisms explain only a subset of PI resistance cases. Hence, we employed a multi-omics approach to identify further molecular pathways underlying PI resistance in MM. Methods: We applied proteomic analysis on PI-naïve parental cell line models and their Bortezomib (BTZ) and Carfilzomib (CFZ) resistant derivatives. RNA-sequencing data and the clinical outcome of MM patients were obtained from CoMMpass to derive the impact of differentially expressed proteins. Identified candidate protein was then overexpressed in MM cell line models and the drug sensitivity changes was measured through Alamarblue. Results: Proteomic screening identified 14 significantly upregulated proteins in CFZ-resistant cells and 9 overexpressed proteins in BTZ-resistant cells. NQO1 was notably overexpressed in both CFZres and BTZres models, confirmed by Western blot and qPCR. To investigate the functional impact of NQO1 on PI sensitivity, we generated NQO1-overexpressing cell lines and assessed their response to BTZ and CFZ. These engineered cell lines exhibited increased IC50 values for both BTZ and CFZ compared to their parental wild-type counterparts, indicating that NQO1 overexpression confers resistance to proteasome inhibition. To validate the clinical relevance of NQO1 expression, we analyzed its impact on progression-free survival (PFS) in MM patients. Specifically, we compared PFS in patients with high NQO1 levels vs. normal/low level, in a subcohort of the CoMMpass dataset (n=409) receiving PI-based first-line therapy. Remarkably, Patients with high NQO1 expression demonstrated significantly shorter PFS (median: 582 days, p &amp;lt; 0.0001) compared to those with normal/low NQO1 levels (median: 1032 days). This adverse prognostic impact was comparable to or even worse than that observed in high-risk myeloma patients with del(17p) (median: 630 days). Importantly, this effect appeared specific to PI-based therapy, as no significant PFS difference was observed between high and normal/low NQO1 expressers in a separate cohort (n=79) receiving PI-free first-line treatment (median PFS: 844 days vs. 1096 days, p = 0.6756). Conclusions: In summary, we identified NQO1 overexpression as a mechanism of proteasome inhibitor resistance in multiple myeloma. Overexpression of NQO1 in vitro confirmed its impact on PI sensitivity, increasing resistance to both BTZ and CFZ. Clinically, high NQO1 expression correlated with significantly shorter PFS in patients receiving PI-based therapy, proposing NQO1 as a functional mediator of PI resistance in MM. Citation Format: Seungbin Han, Chien-Yun Lee, Lenka Besse, Umair Munawar, Shilpa Kurian, Andrej Besse, Ann-Sohpie Hainold, Silvia Nerreter, Cornelia Vogt, Johanna Thurner, Nina Rein, Max Köppel, Xiang Zhou, Larissa Haertle, Christoph Driessen, Hermann Einsele, Leo Rasche, Ondrej Slaby, Johannes Waldschmidt, Bernhard Küster, Klaus Martin Kortüm. Uncovering novel molecular mechanisms of PI resistance in multiple myeloma through multi-omics analysis [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 3079.