Spatiotemporal assessment of immunogenomic heterogeneity in multiple myeloma.

Spatial heterogeneity is a common phenomenon in metastatic solid tumors and an evolving concept in multiple myeloma (MM). The interplay between malignant plasma cells (PC) and the microenvironment has not yet been analysed in MM. For this purpose, we performed bone marrow aspirates and imaging-guided biopsies of corresponding lesions in newly diagnosed (NDMM) and relapsed (RRMM) patients. PC were isolated and subjected to whole-exome sequencing (WES). Non-PC were studied with next-generation flow (NGF) and T-cell receptor sequencing (TCRseq) to analyze the connection between malignant and non-malignant cells in the bone marrow and in lesions. While we observed a strong overlap from WES, NGF and TCRseq in patients with intramedullary disease, WES revealed significant spatial heterogeneity in patients with extramedullary disease. NGF showed significant immunosuppression in RRMM compared to NDMM as indicated by less myeloid dendritic cells (mDC), unswitched memory B-cells, Th9 cells and CD8 effector memory T-cells but more NK and regulatory T-cells. Additionally, less TCR sequences were detected in RRMM compared to NDMM and healthy individuals. After induction therapy, TCR repertoire richness increased to levels of healthy individuals and NGF showed more regulatory T-cells and myeloid derived suppressor cells, regardless of depth of response. Clinical significance of imaging-guided biopsies of lesions was demonstrated by detection of monoclonal PC in patients without measurable residual disease (MRD) in aspirates from the iliac crest as well as identification of secondary primary malignancies in MRD-negative patients. Furthermore, site-specific clones with different drug susceptibilities and genetically defined high-risk features were detected by our workflow.