Single Cell Transcriptomics on Bone Marrow Biopsies Unveils Peculiar Bone Microenvironment Cell Subtypes and Highlights Alterations Correlated with High-Risk Features in Precursor Monoclonal Gammopathies and Multiple Myeloma Patients

• Published in: Blood 2024-11, Vol.144, p.4656-4656
• Main Authors: Dessena, Mattia, Torelli, Tommaso, Manferdini, Cristina, Toscani, Denise, Guidi, Alessandro, Vescovini, Rosanna, Iannozzi, Nicolas Thomas, Dalla Palma, Anna Benedetta, Raimondi, Vincenzo, Lungu, Oxana, Librale, Federica, Bernardi, Matia, Ricci, Stefania, Pelagatti, Laura, Todaro, Giannalisa, Sammarelli, Gabriella, Sitzia, Camilla, Aleo, Emanuela, Lisignoli, Gina, Agnelli, Luca, Giuliani, Nicola, Storti, Paola
• Format: Article
• Language: English
• ISSN: 0006-4971
• DOI: 10.1182/blood-2024-207574

Multiple myeloma (MM) can be preceded by monoclonal gammopathy of undetermined significance (MGUS) and smoldering MM (SMM). In the pathophysiology of MM, the bone microenvironment (BME) plays a pivotal role, but how BME changes contribute to tumor progression in MGUS and SMM remains unresolved. Previous data on BME are mainly produced in vitro from bone marrow (BM) aspirates, and few are on MGUS/SMM patients. To date, no single-cell RNA sequencing database of BME cells has been described in MM. The aim of this project was to characterize, for the first time at single cell level, the BME in patients with MGUS/SMM and newly diagnosed MM (NDMM) to identify high-risk features and alterations involved in tumor progression. From 16 bone biopsies of MGUS, SMM, NDMM patients, we depleted CD235a+, CD45+, CD31+, and CD138+ cells to enrich the rare BME non-hemopoietic cells. The negative cell fractions were analyzed by scRNAseq. Data were generated on Chromium 10X Genomics. Seurat package in R was used for quality check and to identify differentially expressed markers across cell types and clinical conditions. Pathway and biological process (BP) activity inference was performed using EnrichR and GSVA R packages. Trajectory analysis was run with Monocle3 R package. A total of 43154 BME cells were profiled (12.717 from MGUS, 17.230 from SMM and 13.207 from NDMM samples). Within the whole “first-of-its-kind” BME dataset, we identified 16 cell type clusters, all belonging to mesenchymal lineage: 10 clusters showed mesenchymal-stromal features (MSCs) and 4 osteoblast-like (OBs). The peculiar expression of several genes (DKK1, ITGA6, OPG, LEPR, IBSP, WISP2, PDPN, CTSK, CHI3L1) and increased specific BP activity (glycolysis-gluconeogenesis, arachidonic-acid-metabolism, direct ossification, regulation of hematopoietic stem cell proliferation) characterize subtypes of MSCs and OBs. Two further clusters included cells with marked expression of the lncRNA FTX and by IRF1 gene, respectively. Notably, significantly decreased proportion of OB precursors and Mature OB cells, and concomitant significant increase of Proliferating MSC, were found in NDMM. In SMM samples we found an increase of a mesenchymal-cell cluster (MSC1) overexpressing NEAT1 compared to MGUS and a decrease of OB precursors clusters overexpressing LEPR compared to MGUS and MMD samples. Functional analyses revealed that MGUS samples, in MSC clusters, negatively regulated IL-6 production and upregulated immune-stim