Cheloni, Giulia

Abstract Introduction Understanding the tumor immune microenvironment (TIME) in multiple myeloma (MM) is critical for identifying prognostic biomarkers and therapeutic targets. We hypothesized that specific immune cell populations within the bone marrow TIME are associated with clinical outcomes and could enhance patient stratification. To this end, we conducted the largest CyTOF-based immune profiling study to date in MM, profiling >300 million bone marrow immune cells from patients enrolled in the CoMMpass study. Methods We analyzed >1,000 bone marrow samples from ~700 newly diagnosed MM patients enrolled in the MMRF CoMMpass study (NCT01454297), using a harmonized protocol and 41-antibody CyTOF panel at five academic centers. The majority were baseline samples (n=671), with additional samples spanning up to 3.5 years post-diagnosis (n>300). Each site contributed ~200 samples on average. The cohort included 40% females, with a median age of 63 years and BMI of 27.8. ISS stages were evenly distributed (I: 36%, II: 36%, III: 29%), and 84% had ECOG 0-1. Autologous stem cell transplant was performed in 58% of patients, and 22% received maintenance therapy. Results We profiled 311 million single cells across the cohort, identifying major immune compartments: Neutrophils (36.0%), CD4 T cells (19.7%), NK cells (9.9%), monocytes (7.6%), B cells (5.7%), and CD8 T cells (5.6%). Less abundant populations included dendritic cells, γδ T cells, plasmablasts, and pDCs. In our preliminary analysis with multivariate cox regression modeling, we identified clinical factors including stem cell transplant, ISS stage, and ECOG status, as independent predictors of overall survival (OS). After adjusting for age and sex, higher proportions of naïve B cells, pDCs, and γδ T cells were independently associated with improved OS, while CD4+ T cell abundance was positively associated with prolonged progression-free survival (PFS). In contrast, elevated neutrophil proportions were significantly linked to inferior OS and demonstrated a trend toward shorter PFS. Longitudinal immune profiling in more than 200 patients identified a gradual accumulation of naïve B cells and a pronounced post-treatment rise in CD45+ plasmablasts, highlighting persistent B cell activity as a candidate mechanism for sustained therapeutic efficacy. Conclusion This study presents the largest immune proteomic atlas in MM to date, linking TIME composition to clinical outcomes. A favorable immune landscape was marked by preserved humoral immunity (naïve B cells, plasmablast expansion), enrichment of pDCs and γδ T cells, and lower neutrophil abundance, collectively associated with improved survival outcomes. These findings lay the groundwork for immune-guided prognostication and highlight new opportunities for therapeutic targeting in MM. Ongoing analyses aim to further resolve baseline and longitudinal immune dynamics in relation to treatment response.

As part of the Multiple Myeloma Research Foundation (MMRF) immune atlas pilot project, we compared immune cells of multiple myeloma bone marrow samples from 18 patients assessed by single-cell RNA sequencing (scRNA-seq), mass cytometry (CyTOF), and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to understand the concordance of measurements among single-cell techniques. Cell type abundances are relatively consistent across the three approaches, while variations are observed in T cells, macrophages, and monocytes. Concordance and correlation analysis of cell type marker gene expression across different modalities highlighted the importance of choosing cell type marker genes best suited to particular modalities. By integrating data from these three assays, we found International Staging System stage 3 patients exhibited decreased CD4+ T/CD8+ T cells ratio. Moreover, we observed upregulation of RAC2 and PSMB9, in natural killer cells of fast progressors compared with those of nonprogressors, as revealed by both scRNA-seq and CITE-seq RNA measurement. This detailed examination of the immune microenvironment in multiple myeloma using multiple single-cell technologies revealed markers associated with multiple myeloma rapid progression which will be further characterized by the full-scale immune atlas project. Significance: scRNA-seq, CyTOF, and CITE-seq are increasingly used for evaluating cellular heterogeneity. Understanding their concordances is of great interest. To date, this study is the most comprehensive examination of the measurement of the immune microenvironment in multiple myeloma using the three techniques. Moreover, we identified markers predicted to be significantly associated with multiple myeloma rapid progression.