Characterization of Plasma and Immune Cells Molecular Landscape That Play a Role in Rapid Progression of Multiple Myeloma Using Cross Center Scrna-Seq Study

Introduction: Multiple myeloma (MM) is a genetically complex and clinically heterogeneous disease. Disease biology and phenotype is heavily influenced by the tumor microenvironment and the interaction between the immune milieu and malignant plasma cell population. Understanding the molecular profile of tumor along with the immune ecosystem can provide insights into key pathways that are important in disease pathobiology. Therefore, in this study, we have used single-cell RNA-Seq (scRNA-Seq) to compare the detailed maps of the bone marrow microenvironment of patients with rapid progressing disease (PFS < 18 months) with those whose disease had not progressed at the time of analysis (PFS < 4 years)

Methods: MM patients (n=18) with rapid and no progression were identified from the Multiple Myeloma Research Foundation (MMRF) CoMMpass study, a longitudinal genomic study of patients with newly diagnosed, active multiple myeloma (NCT01454297). To generate a robust scRNA-Seq profile with minimal false positive, we profiled multiple technical replicates/aliquots of viably frozen CD138-negative bone marrow cells from each patient at three medical centers/universities (Beth Israel Deaconess Medical Center, Boston, Washington University in St. Louis and Mount Sinai School of Medicine, NYC using droplet-based single-cell barcoding technique. After batch correction and normalization, the cellular clusters were identified using principal component analysis and Uniform Manifold Approximation and Projection (UMAP) approach (Becht et al, 2018). Differential expression, pathways and systems biology analysis between rapid and non-progressors revealed differences for specific cell clusters (Panigrahy, Gartung et al. 2019). To determine association of plasma cell overexpressed genes with survival in CoMMpass study, survival analysis was performed using Kaplan-Meier (K-M) approach.

Results: In this study, comparative analysis was performed of the bone marrow microenvironment of patients with aggressive and indolent disease by generating single-cell profiles of ~102,207 cells from 48 samples of 18 patients with MM. The UMAP approach identified multiple transcriptionally diverse clusters of plasma (CD138+), immune (PTPRC+) and erythroid (GYPA1/2+) cells (Fig 1a). Interestingly, the analysis identified CD138+ plasma/tumors cells clusters in a subset of samples from patients with rapid -progression and these clusters depicted a high degree of inter-patient heterogeneity (Fig 1a). Further characterization of plasma tumor cells depicted significant activation (Z score >2 and P-value <.001) of pathway related to “Unfolded protein response”, epithelial-mesenchymal transition (EMT), and “p38 MAPK Signaling”. These rapid progressions associated with plasma cells overexpressing multiple genes (e.g., Hazard ratio (HR) CCL3=1.9 95% CI= (1.5-3.9) log-rank P=0.0004, HSPA5 HR=1.4 (1-2.6), P=0.03) that are associated with poor outcome in multiple myeloma based CoMMpass data. The bone marrow microenvironment cells formed 22 clusters, comprising of cells from myeloid, macrophages, T cells, B cells, dendritic cells, Natural Killer T (NKT) cells, and erythroid lineages. The Non-progressive patients depicted enrichment of GZMB+ T and NKT cells with overexpression of genes associated with “Natural Killer Cell Signaling”, “CD28 Signaling in T Helper Cells”, “NF-kB Signaling” and “Th17 Activation Pathway” (Fig1b, c). Systems biology analysis depicted significant activation of TNF, STAT4, and NFATC2 regulatory signatures in NKT cells. The analysis also observed enrichment of macrophages, several types of monocytes, and myeloid cells in the samples from patients with non-progressive disease (Fig 1d). The myeloid/monocytes cluster depicted significant activation of multiple metabolic (i.e., Glycolysis, Gluconeogenesis) and immune response (i.e. IL8) pathways (Fig 1e).

In summary, this multi-site study provides insights into potentially significant differences in the transcriptomic landscape of multiple myeloma patients with rapid and non-progression of disease. The non-progressive patients depict significant enrichment of activated T cells and myeloid lineage populations, suggesting their role toward better outcomes. These findings will be further expanded by ongoing single cell analyses of the CoMMpass tissue bank under the MMRF Immune Atlas initiative.