Mapping Cell-Cell Communication Dynamics Across the Spectrum of Multiple Myeloma Evolution Using Single-Cell Transcriptomics

Abstract

Introduction: Multiple myeloma (MM) is a malignancy marked by clonal proliferation of plasma cells (PCs) in the bone marrow (BM), progressing through MGUS, SMM, and symptomatic MM. While tumor-intrinsic features are well-studied, less is known about howBMcell–cell communication evolves during disease. Intercellular signaling plays a critical role in tumor progression and immune evasion. We used MultiNicheNet, a computational tool integrating ligand-receptor expression with downstream transcriptional responses, to investigate how communication between immune and stromal cells is remodeled across disease stages compared to healthy donors (HD). Methods:We analyzed scRNA-seq data from 12 GEO datasets comprising HD (n = 54), MGUS (n = 25), SMM (n = 14), and MM (n = 85), totaling over 434,000 BM cells after downsampling to a maximum of 1,000 cells per patient. Cell types were annotated and MultiNicheNet was used to infer differential communication (up- and down-regulated ligand-receptor pairs) between each disease stage and HD. For each comparison, the 50 most significant upregulated and downregulated interactions were identified and categorized by sender and receiver cytotypes, recurrence, and disease stage specificity. Results: We observed distinct alterations in cell–cell communication across stages. Among the most recurrent downregulated interactions were S100A8–CD69 and ANXA1–FPR1 (shared in MGUS/SMM), and TYROBP– TREM1, suppressed in all stages and primarily involving monocytes. Stage-specific losses included ADAM17–ITGB1 (MGUS), S100A9– ITGB2 and ICAM1–ITGB2 (SMM), and CLEC2D–KLRB1 and TNFSF13B–TNFRSF13B (MM), affecting NK, T cells, PCs and myeloid lineages. Among upregulated interactions, PTPRC–CD247 emerged as a consistent feature across all stages in NK-related circuits (e.g., NK–NK, CD8–NK). MGUS showed early NK activation signals (e.g., TGFB1–TGFBR3, ICAM3–ITGAL), while, in SMM stage, PCs showed increased inhibitory interactions such as BST2– LILRB3/LILRA5 with CD16+ cells. MM was marked by classical monocyte-driven inflammatory signals such as S100A8/A9/A12– TLR4, IFNG–IFNGR2, and ANXA1–FPR1. Abundance analysis showed enrichment of NK cells in MGUS, while plasma cells were increased in SMM and MM. Monocyte levels remained stable. Conclusions: This study maps dynamic shifts in BM intercellular signaling during MM evolution, highlighting conserved (e.g., PTPRC–CD247) and stage-specific ligand-receptor axes. MGUS features NK-centered signaling, SMM shows rising inhibition and plasmacytoid involvement, and MM exhibits myeloid-driven inflammation. While functional implications remain to be fully defined, these findings point to novel therapeutic avenues and biomarkers tailored to disease stage.