Profiling the Cell Surface Landscape of Proteasome Inhibitor-Treated and -Resistant Multiple Myeloma to Guide Immunotherapy Targeting, Diagnosis, and Biology
Authors: Ferguson Ian , Lin Yu-Hsiu T. , Tuomivaara Sami , Wolf Jeffrey L. , Martin Thomas G. , Wong Sandy W. , Shah Nina D. , Driessen Christoph , Van Ness Brian G. , Wiita Arun P. 
Published: November 2019

Introduction: Proteasome inhibitor (PI) resistance remains a major clinical challenge in multiple myeloma (MM). As the proteasome plays a central role in cellular protein homeostasis, we hypothesized both PI treatment and resistance might rewire protein transport and recycling pathways, thereby leading to broad changes in cell surface protein expression. Defining the cell surface proteome has become increasingly important in MM to quantify immunotherapy target expression, identify potential biomarkers of drug response or resistance, and reveal proteins mediating interaction with the tumor microenvironment. Unbiased mass spectrometry approaches allow for profiling of hundreds of surface proteins simultaneously, allowing for novel protein discovery and extending beyond the limits of flow or mass cytometry.
Methods: PI-resistant cells derived from cell lines AMO-1, L363, and RPMI-8226, and ARH-77 were grown in 90nM Bortezomib or Carfilzomib as previously described (Soriano et al, Leukemia (2016)). N-glycoproteomics was performed in triplicate on PI-resistant and parental lines. Briefly, glycosylated cell surface proteins were biotinylated prior to enrichment with Neutravidin beads and downstream LC-MS analysis. For perturbation studies, AMO-1 and RPMI-8226 cells were treated for 48 hours with Bortezomib, Lenalidomide, or CB-5083 prior to N-glycoproteomics. Flow cytometry was performed to validate surface protein abundance changes in PI-resistant lines, as well as with MM cell lines and ex vivo MM patient bone marrow mononuclear cells (PBMCs) treated with bortezomib and lenalidomide. For ex vivo MM patient cell surface proteomics, plasma cells were isolated from PBMCs with anti-CD138 magnetic beads prior to N-glycoproteomic analysis. Mass spectrometry data was analyzed in Maxquant and statistical analysis was performed in Perseus and R.
Results: Supporting our hypothesis, we found that the MM surfaceome is broadly re-wired in the PI-resistant state. Using N-glycoproteomics, we identified EVI2B, CD53, CD50, and ITGB7 as downregulated and CD151, CD10, and SERC3 as upregulated in PI-resistant myeloma cell lines (up and downregulated defined as at least a +/- log2 fold change of 1.5 and p < .05). Notably, ITGB7 is under development as an immunotherapy target for MM (Hosen et al, Nat Med (2017)). To understand how surface remodeling in the PI-resistant state compares with short-term exposure to PI, we treated MM cells with bortezomib and again found broad surfaceome remodeling, including loss of immunotherapy target BCMA. We identified GITR, CD53, and ITGB7, among other proteins, as downregulated in both bortezomib-exposed and PI-resistant MM, suggesting that expression of proteins involved in therapeutic resistance might be rapidly modulated in initial cycles of therapy. To compare surfaceome changes identified in PI-exposure and resistance and those seen under anti-MM therapeutics with alternative mechanisms of action, we performed N-glycoproteomics on MM cells treated with the clinical immunomodulating agent Lenalidomide and the cytotoxic p97/VCP inhibitor CB-5083. Interestingly, we found MUC1, a proposed myeloma oncoprotein, to be upregulated under lenalidomide in AMO-1 but downregulated in the PI-resistant state. We validated surface protein abundance changes in PI-resistant MM cell lines and drug-treated MM cell lines or ex-vivo MM patient samples by flow cytometry. For additional validation, we are currently optimizing methods for N-glycoproteomics on CD138+ cells isolated from primary MM patient bone marrow aspirates. Initial results suggest several markers identified in cell lines are also highly expressed in primary PI-resistant MM.
Conclusions: Unbiased N-glycoproteomics reveals broad cell surface protein remodeling in PI-resistant MM. Short-term treatment with bortezomib or lenalidomide also leads to significant surface alterations, with differential expression of proteins including MUC1, GITR, and BCMA potentially playing a role in drug resistance and informing rational combination with immunotherapies.

Disclosures
Martin: Roche and Juno: Consultancy; Amgen, Sanofi, Seattle Genetics: Research Funding. Wong:Celgene: Research Funding; Janssen: Research Funding; Roche: Research Funding; Fortis: Research Funding. Wiita:Indapta Therapeutics: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Protocol Intelligence: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; UCSF: Patents & Royalties.