GSE210079
Changes in bone marrow tumor and immune cells correlate with durability of remissions following BCMA CAR T therapy in myeloma
Chimeric antigen-receptor (CAR) T cells targeting B-cell maturation antigen (BCMA) lead to high response rates in myeloma, but most patients experience recurrent disease. We combined several high-dimensional approaches to study tumor/immune cells in the tumor microenvironment of myeloma patients pre- and post-BCMA-specific CAR T therapy. A lower diversity of pre-therapy T-cell-receptor (TCR) repertoire, presence of hyperexpanded clones with an exhaustion phenotype, and BAFF+PD-L1+ myeloid cells in the marrow correlated with shorter progression-free survival (PFS) following CAR T therapy. In contrast, longer PFS was associated with increased proportion of CLEC9A+ dendritic cells (DCs), and CD27+TCF1+ T cells with diverse T-cell receptors, followed by emergence of T cells expressing marrow-residence genes. Residual tumor cells at initial response express stem-like genes and tumor recurrence in patients with long PFS was associated with emergence of new dominant clones. These data illustrate dynamic interplay between endogenous T, infused CAR T, myeloid/DC and tumor compartments that impacts durability of response following CAR T therapy in myeloma. Overall design: Bone marrow mononuclear cells (BMMNCs) were obtained from Multiple Myeloma (MM) patients before and after therapy with BCMA CAR T therapy. Bone marrow mononuclear cells (BMMNCs) were isolated using density gradient centrifugation followed by cryopreservation. Thawed BMMNCs were stained with custom panels of metal-conjugated antibodies at manufacturer-suggested concentrations (Fluidigm). Viable cells and doublets were excluded using cisplatin intercalator and DNA content with iridium intercalator. Equal numbers of cells from each donor were utilized when data were concatenated prior to analysis. Gene expression, cell surface, and TCR libraries were prepared according to the protocol from 10X Genomics. The quality of the prepared libraries was assessed using the Agilent HS Bioanalyzer 2100 and sequencing was conducted on an Illumina NovaSeq 6000.