Single-Cell Transcriptomic and Proteomic Diversity in Multiple Myeloma

Multiple myeloma (MM) is a disease defined by clonal proliferation of abnormal plasma cells from B-cells. Improved treatments for MM have led to improving overall lifespan, but still remains incurable due to acquired resistance to therapy and tumor heterogeneity. Single-cell RNA sequencing studies (scRNA-seq) of MM patients have highlighted the significant inter-individual heterogeneity and subclonal architecture of the malignant plasma cell populations, emphasizing the importance of developing personalized therapies specific to a patients molecular pathogenesis. In this study, we have integrated scRNA-seq with single-cell proteomics (sc-Prot) for 10 plasma cells and CD4+ T cells to validate and prioritize driver events in malignant cells and evaluate the tumor microenvironment. This effort will be expanded to another 10 cases to further integrate scRNA-seq, snATAC-seq, whole exome sequencing and bulk RNA-sequencing on a fraction of the cells isolated from bone marrow. The remaining cells will be sorted using FACS to select for specific malignant and immune cells including 40 plasma cells, 15 CD4+ T and 15 CD8+ T cells. These sorted cells will be profiled with a scProt technology (BASIL nanoPOTS) to illuminate their cell-to-cell heterogeneity. In our pilot study comparing bulk and single-cell proteomic data of a single patient's plasma cells (CD138+) for 400 representative proteins, while a majority of expression signatures are concurrent between the two methods, some signaling pathways including translation and apoptotic cleavage are discordant. Our findings stress the importance of interrogating subpopulations of immune and malignant cells at the single-cell level to further refine the transcriptomic and proteomic heterogeneity of MM in a cell type specific manner. With the aid of single-cell technology, we have assessed the heterogeneity of malignant and immune cell types to evaluate transcriptomic and proteomic changes contributing to altering the interplay between the immune environment and tumor cells.