Comprehensive Characterization of the Plasma Proteome of Multiple Myeloma and Its Precursor Conditions and Identification of a Proteomic Signature to Improve Risk Prediction of Disease Progression

Introduction

Multiple Myeloma (MM) precursors Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smoldering Multiple Myeloma (SMM) have variable risk of progression to active MM, and identifying which patients may progress remains a clinical challenge. Deep proteome profiling of peripheral blood (PB) plasma may advance non-invasive precursor disease staging, monitoring and characterization. Here, we performed plasma proteomic profiling on patients across the MM disease continuum as well as progressive and stable disease to provide insights into MM disease biology and identify protein-based high-risk disease features that may improve prognostication.

Methods

We performed high-throughput profiling of >5400 proteins using the Olink® Explore HT library and Proximity Extension Assay (PEA) technology. We profiled 529 PB plasma samples from 485 individuals, including MGUS (n=100), SMM (n=203), MM (n=100), and healthy donors (HDs) (n=82). Sequential samples from SMM-MM progressors (n=32) and stable SMM-SMM non-progressors (n=32) were also profiled, where precursor samples ranged 1.04-6.91 years (median 2.33 years) prior to MM progression. T-tests, ANOVAs, and linear mixed effect (LME) models were used to identify significant proteins across disease stages, progression status, and time. Results were adjusted for multiple testing using Benjamini-Hochberg procedure. A subset of 86 individuals (13 HDs, 14 MGUS, 41 SMM, 18 MM) also had single-cell RNA sequencing (scRNA-seq) performed on tumor and immune cells from paired PB/BM collected at the same timepoint to enable cellular mapping of signals detected in plasma.

Results

We successfully captured significantly dysregulated proteins including proteins highly expressed on the surface of plasma cells, such as BCMA, SLAMF7 and CD38, highlighting the utility of PEA technology to monitor soluble levels of clinically relevant targets. Given SMM patients are clinically heterogeneous and can resemble MGUS or MM, we aimed to improve discrimination of disease states using biological features obtained from the plasma proteome. We developed a classifier using an Elastic Net model for each stage, where plasma proteins such as SLAMF7, BCMA, TACI, FCRL5 and others had the highest importance scores for the model. We demonstrated 97% SMM/MM samples could be identified from healthy samples (AUC=0.82), indicating our classifier could reliably screen disease-related cases. Moreover, 84% of SMM cases were correctly classified as clinically defined SMM, while misclassified samples were labelled as MM cases. Interestingly, the misclassified patients had consistently rising M-spike levels during clinical follow-up but without a shift in clinical stage or risk status, suggesting the plasma proteome may provide earlier indication of evolving disease.

Since proteomic information may also hold value for improved risk stratification, we evaluated protein levels in precursor stage timepoint samples from SMM-MM progressors and stable SMM non-progressors. We identified a prognostic five-protein signature that was significantly elevated in SMM-MM progressors, of which BCMA and TACI were top proteins, as well as proteins vital for calcium homeostasis and integrin-mediated cell adhesion. BCMA and TACI levels also had a strong positive correlation with BM plasma cell infiltration, which suggests these proteins may be useful surrogates of BM tumor burden during routine blood-based assessment of precursor patients. Lastly, integrative analysis of scRNA-seq of tumor and immune cells was used to elucidate cell origin level information of the prognostic signature proteins. Four proteins were highly expressed in malignant versus non-malignant plasma cells, suggesting our prognostic signature partially provides a readout of plasma cell biology. Meanwhile, one protein was constitutively expressed on most leukocytes, suggesting that the interplay of other cell types in the immune microenvironment involved in progression may also be reflected in the plasma.

Conclusion

We performed the first comprehensive analysis of the plasma proteome of MM and its precursor conditions. Overall, we developed a classifier that utilizes plasma proteins alone to accurately classify disease stages and identified a prognostic protein signature associated with progressive disease.

Sklavenitis-Pistofidis:PreDICTA Biosciences: Consultancy, Current equity holder in private company, Other: Co-founder. Marinac:Exact Sciences: Membership on an entity's Board of Directors or advisory committees; Natera: Membership on an entity's Board of Directors or advisory committees. Getz:PreDICTA Biosciences: Consultancy, Current equity holder in private company, Other: Founder; Scorpion Therapeutics: Consultancy, Current equity holder in private company, Other: Founder; Broad Institute: Patents & Royalties: MSMuTect, MSMutSig, POLYSOLVER, SignatureAnalyzer-GPU, MSEye, and MinimuMM-seq; IBM, Pharmacyclics/Abbvie, Bayer, Genentech, Calico, and Ultima Genomics: Research Funding. Carr:PrognomIQ: Membership on an entity's Board of Directors or advisory committees; Seer: Membership on an entity's Board of Directors or advisory committees; PTM BioLabs: Membership on an entity's Board of Directors or advisory committees; Kymera: Membership on an entity's Board of Directors or advisory committees. Ghobrial:GlaxoSmithKline: Consultancy; Janssen: Consultancy, Other: Speaker fees; Sognef: Consultancy; Oncopeptides: Consultancy; Bristol Myers Squibb: Consultancy, Other: Speaker fees; Novartis: Consultancy; Adaptive: Consultancy; Menarini Silicon Biosystems: Consultancy, Other: Speaker fees; AbbVie: Consultancy; Takeda: Consultancy, Other: Speaker fees; Regeneron: Consultancy, Other: Speaker fees; Binding Site, part of Thermo Fisher Scientific: Consultancy; CurioScience: Consultancy, Other: Speaker fees; Window Therapeutics: Consultancy; 10X Genomics: Consultancy; Vor Biopharma: Other: Speaker fees; Standard Biotools: Other: Speaker fees; Amgen: Consultancy, Other: Speaker fees; PreDICTA Bioscience: Consultancy, Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees, Other: Co-founder; Disc Medicine: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Huron Consulting: Consultancy; Aptitude Health: Consultancy; Pfizer: Consultancy, Other: Speaker fees; Sanofi: Consultancy.