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    Myeloma Genomics and Microenvironment and immune profiling

    Category: Myeloma Genomics and Microenvironment and immune profiling

    Temporal and Spatial Determinants of CAR-T Cell Therapy Efficacy in Multiple Myeloma

    (PA-263) Temporal and Spatial Determinants of CAR-T Cell Therapy Efficacy in Multiple Myeloma

    Friday, September 19, 2025
    Introduction: While chimeric antigen receptor (CAR) T therapy offers promise for relapsed/refractory multiple myeloma (MM) patients, disease recurrence remains problematic. Delineating the mechanisms behind CAR T cell failure is essential for enhancing therapeutic efficacy and achieving durable remissions. To this end, we evaluated the spatial transcriptomes of longitudinal MM cases to understand the immune and tumor landscape during CART treatment and uncover fundamental mechanisms and spatial biomarkers that may guide the development of more effective CAR T cell therapies.

    Methods:

    We utilized Xenium spatial transcriptomics on pre and post CAR T bone marrow biopsies treated with BCMA CART. All samples were run using the Human Multi-Tissue and Cancer panel (377 genes) with a custom 100 genes added. To reduce batch effects, paired specimens were run on the same slide and processed using the Xenium Multi Tissue Stain protocol to aid cell segmentation followed by H&E staining. Samples were all processed using Xenium instrument software for cell segmentation and probe deconvolution followed by downstream analysis in R utilizing Seurat and custom scripts. To annotate the cell types, we first performed label transfer (via Seurat functions FindTransferAnchors and MapQuery) using both internal and external MM single-cell datasets. We then manually evaluated cell type annotation based on marker gene expression. Image-based analysis of Xenium samples following cell type assignment was performed using the Xenium Explorer desktop application (10x Genomics).

    Results:

    We assayed over one million cells across 20 samples, including 7 paired pre/post CART, 5 pre-CART and 1 post-CAR T singletons using the Xenium platform. Treatment response for paired samples included 1 complete response (CR), 3 partial response (PR), 3 progressive disease (PD). All singletons had PD. Cells spanned the following lineages: lymphoid, megakaryocyte/erythroid, myeloid and stromal compartments with more granular cell annotation encompassing adipocytes, osteoblasts, and mesenchymal stem cells, among others. The myeloid lineage represented the largest proportion of cells (range: 25%-50%). CAR T treatment in the PR patients led to a notable decrease in B and plasma cells while patients with PD exhibited an increase in the same compartments post-CAR T and plasma cells continued to express TNFRSF17 (i.e. BCMA). Additionally, a majority of post-CAR T samples showed a modest increase in stromal cells, although specific stromal subtypes varied across patients. We observe megakaryocyte dense regions and plasma cells located in two spatial orientations, spatially diffuse and spatially dense and do not observe differences in the two spatial stratification patterns associated with treatment response. 

    Conclusions: Longitudinal spatial profiling of MM during treatment can identify microenvironmental structures that may either hinder or support disease responses to CAR T therapy. Additional data is needed for detailed clinical correlation.