Single-Cell Transcriptome Profiling Reveals Tumor Cell Heterogeneity and Immunosuppressive Microenvironment in Waldenström Macroglobulinemia

Abstract

Purpose: In this study, we delineated the multicellular ecosystem in bone marrow (BM) of Waldenström macroglobulinemia (WM), and elucidate the immune cell dysfunction, which would provide novel insights into the disease development and progression. Experimental Design: BM samples from 6 healthy donors and 14 patients were subjected to scRNA-seq using 3' or 5' mRNA & TCR & BCR library and further analysis. Results: ScRNA-seq analysis provides a comprehensive single-cell transcriptomic atlas to characterize cellular ecosystems in WM BM. We firstly delineated a novel model for the ecosystem of WM, wherein tumor cells and immune cells co-evolve kinetically, and clarified an aberrant immune suppressive milieu. Besides malignant B cells, malignant plasma cells, and plasmacytoid lymphocytes, two novel sub-populations co-expressing T-cell marker genes, CD19+CD3+ and CD138+CD3+ cells were identified with distinct transcriptomic profiles. CD19+CD3+ malignant cells present an early stage of B cell differentiation compared with CD19+CD3- canonical B cells. Colony formation assay further identified that CD19+CD3+ malignant cells acted as potential WM precursors. Moreover, we observed tumor-derived perturbations of T cells in WM milieu. A precursor exhausted CD8-T cells and functional deletion of natural killer cells were identified, which was involved in the development of an immunosuppressive microenvironment. Our study indicated that CD47 would be a potential therapeutic target to reverse immune cell dysfunction in WM. Conclusions: Our study identified the biological heterogeneity of malignant cells and the altered functional states of immune cells in WM. This integrative analysis provides novel insights into the pathogenesis of WM and enhances the rational development of precision therapies to benefit patients with the greatest need.