Dissecting the multiple myeloma survival niche to improve novel treatment strategies

Multiple myeloma (MM) is the second most common hematologic malignancy. Although novel treatment options, including immunotherapies, have significantly improved survival in recent years, it remains an incurable disease. 15% of newly diagnosed patients have high-risk (HR) genomic alterations and have limited overall survival and an increased risk for (fatal) infectious complications. This may indicate an association between HR disease and impaired immune function. In addition, the presence of extramedullary disease (EMD) is a poor prognostic marker, as no specific treatment is available until now and the response rate to novel T-cell engaging therapies is approximately halved in patients with EMD. Thus, we hypothesized that HR disease in MM confers a degree of T-cell dysfunction that translates into an increased rate of infection and decreased response rates to T-cell-based therapies. To address this hypothesis, we investigated the tumor microenvironment in the bone marrow (BM) in dependency of risk status and in EMD. Immune cells and inhibitory metabolites may play a role in the MM niche. To examine these in the BM, we used flow cytometry (n=162), single-cell RNA sequencing (scRNAseq) (n=19), and analysis of water-soluble metabolites (n=49) by liquid chromatography-mass spectrometry. Significant differences in the T cell composition were found, with a decrease in the proportion of CD3e+ T cells in HR patients, and a reduction of naïve T cells following treatment in both risk statuses. T cells of treated HR patients upregulated apoptosis, whereas standard-risk (SR) T cells upregulated oxidative phosphorylation. When comparing metabolites, untreated HR patients showed decreased glutamine and arginine levels. To investigate the cellular niche of EMD in the spatial context, we performed spatial transcriptomics (RNA tomography for spatially resolved transcriptomics tomo-seq n = 2 and 10x Visium n = 12) and scRNAseq (n = 3) on a total of 14 EMD samples. Immune infiltration was observed in some patients, where exhausted TIM3+/PD-1+ T cells were found in close proximity to the plasma cells (PC), while active and functional CD8+ T cells and M1 macrophages accumulated in specific niches. Importantly, this finding was also seen in patients who responded to bispecific antibody therapy. We further used the transcriptomics data to predict copy number variation. Clonal heterogeneity was observed at the copy number level, indicating the emergence of new subclones, and by the expression of the PC markers tumor necrosis factor receptor superfamily member 17 (TNFRSF17) (encoding B cell maturation antigen (BCMA)) and G protein-coupled receptor class C group 5 member D (GPRC5D). Taken together, our findings illustrate a hallmark of HR disease that goes beyond genomic alterations in tumor cells, encompassing differences in T cell frequencies and functions, suggesting the benefit of earlier chimeric antigen receptor T cell (CAR-T) production in HR patients. Our study provides evidence supporting metabolic alterations in the BM microenvironment as a key driver of these pathological processes. Finally, a novel therapeutic approach for EMD may be the dual targeting of PC markers with simultaneous checkpoint inhibition.