Single-cell analysis of the tumor microenvironment landscape across the disease spectrum of multiple myeloma

Abstract Multiple myeloma (MM) progresses from precursor states to active disease, and studying tumor microenvironment (TME) evolution across these stages is key to understanding immune dysregulation and therapeutic resistance. Here, we integrated paired single-cell RNA and T- and B-cell receptor sequencing data from bone marrow (BM) samples of 235 patients spanning the disease spectrum. This data set revealed dynamic changes in the abundance and functional states of diverse immune populations, including T, natural killer, B, and myeloid cells. Using nonnegative factorization of cell-subset composition, we identified 5 reproducible TME subtypes, or “ecotypes,” defined by coordinated cellular architectures. These ecotypes captured structured variation beyond disease stage and were associated with distinct cell-cell communication networks, cytokine signaling landscapes, transcription factor programs, and shared gene modules, reflecting a coordinated immune adaptation to microenvironmental constraints. By linking tumor features with immune changes and ecotype distributions, we identified context-dependent associations influenced by both disease biology and treatment effects on the TME. We found that an ecotype enriched for BM-resident populations and limited immune infiltration was associated with tumor expansion and inferior clinical outcomes, whereas ecotypes reflecting T-cell functional states showed distinct associations with immunotherapy response and survival. Our study provides a comprehensive single-cell immune atlas of MM and its precursors, offering insights into TME organization and progression, and may guide the development of stage-specific or ecotype-targeted immunotherapies.