Hallmarks of tumor-experienced T cells are absent in multiple myeloma patients from diagnosis through maintenance therapy

Abstract

Dysregulation of the bone marrow (BM) niche in multiple myeloma (MM) alters the composition and state of resident immune cells, potentially impeding anti-tumor immunity. One common mechanism of immune inhibition in solid tumors is the induction of exhaustion in tumor-specific T cells. However, the extent of T cell tumor recognition and exhaustion is not well-characterized in MM. As the specific mechanisms of immune evasion are critical for devising effective therapeutic strategies, we deeply profiled the CD8⁺ T cell compartment of newly-diagnosed MM (NDMM) patients for evidence of tumor reactivity and T cell exhaustion. We applied single-cell multi-omic sequencing and antigen-specific mass cytometry to longitudinal BM and peripheral blood (PB) samples taken from timepoints spanning from diagnosis through induction therapy, autologous stem cell transplant (ASCT), and maintenance therapy. We identified an exhausted-like population that lacked several canonical exhaustion markers, was not significantly enriched in NDMM patients, and consisted of small, nonpersistent clones. We also observed an activated population with increased frequency in the PB of NDMM patients exhibiting phenotypic and clonal features consistent with homeostatic, antigen-nonspecific activation. However, there was no evidence of "tumor-experienced" T cells displaying hallmarks of terminal exhaustion and/or tumor-specific activation/expansion in NDMM patients at any timepoint.

Figure 1:. Hallmarks of tumor-experienced T cells are absent in NDMM.

1A: Experimental diagram and clinical time course. ADT=antibody-derived tag; GEX=gene expression; TCR=T cell receptor. 1B: TotalVI-UMAP of CD8⁺ T cells colored by cluster. 1C: Mean expression of proteins (top) or genes (bottom) by cluster. 1D: TotalVI-UMAP of CD8⁺ T cells colored by gene set score. 1E: Mean gene set score by cluster. 1F: PRETX frequency of exhausted-like/exhausted T cells quantified by single-cell sequencing, including public data,^– and separated by tumor type; p calculated by Wilcoxon rank sum test. AML=acute myeloid leukemia; CRC=colorectal cancer; LC=lung cancer; EC=esophageal cancer; BCL=B cell lymphoma. 1G: PRETX frequency of PD-1⁺⁺CD39⁺ T cells quantified by mass cytometry, including public data, and separated by tumor type; p calculated by Wilcoxon rank sum test. 1H: Frequency of exhausted-like (left) or activated (right) cells in NDMM patients at PRETX and healthy controls, by tissue; p calculated by Wilcoxon rank sum test. 1I: Frequency of BM (left panel) or PB (right panel) exhausted-like or activated cells (x-axis) and BM tumor cells quantified by clinical immunohistochemistry (y-axis) at PRETX; r and p calculated by Spearman method. 1J: PRETX frequency of pMHC-tet⁺CD8⁺ T cells by peptide family and tissue; lines grouped by patient.

Figure 2:. Activated and exhausted-like cells lack clonal features typical of tumor-experienced T cells.

2A: Frequency of BM tumor cells quantified by clinical immunohistochemistry, separated by timepoint; lines grouped by patient. 2B: Frequency of exhausted-like or activated cells by timepoint and tissue; lines grouped by patient; p calculated by Wilcoxon rank sum test. 2C: TotalVI-UMAP colored by clone size (left) or population (right). 2D: Frequency of expanded clones in NDMM patients by population; lines grouped by patient; p calculated by Wilcoxon rank sum test. 2E: Percent of bystander-specific clones in NDMM patients by population. 2F: Jaccard similarity of clonal composition in NDMM patients by population. 2G: Number of clones by population and timepoint, colored by clonal persistence at later timepoints. 2H: Circos plot by population and timepoint. Bar size indicates number of cells and lines indicate number of clonal connections.