Identification of potential resistance mechanisms and therapeutic targets for the relapse of BCMA CAR-T therapy in relapsed/refractory multiple myeloma through single-cell sequencing

Abstract

Background BCMA CAR-T is highly effective for relapsed/refractory multiple myeloma(R/R-MM) and significantly improves the survival of patients. However, the short remission time and high relapse rate of MM patients treated with BCMA CAR-T remain bottlenecks that limit long-term survival. The immune microenvironment of the bone marrow (BM) in R/R-MM may be responsible for this. The present study aims to present an in-depth analysis of resistant mechanisms and to explore potential novel therapeutic targets for relapse of BCMA CAR-T treatment via single-cell RNA sequencing (scRNA-seq) of BM plasma cells and immune cells. Methods This study used 10X Genomic scRNA-seq to identify cell populations in R/R-MM CD45+ BM cells before BCMA CAR-T treatment and relapse after BCMA CAR-T treatment. Cell Ranger pipeline and CellChat were used to perform detailed analysis. Results We compared the heterogeneity of CD45+ BM cells before BCMA CAR-T treatment and relapse after BCMA CAR-T treatment. We found that the proportion of monocytes/macrophages increased, while the percentage of T cells decreased at relapse after BCMA CAR-T treatment. We then reclustered and analyzed the alterations in plasma cells, T cells, NK cells, DCs, neutrophils, and monocytes/macrophages in the BM microenvironment before BCMA CAR-T treatment and relapse after BCMA CAR-T treatment. We show here that the percentage of BCMA positive plasma cells increased at relapse after BCMA CAR-T cell therapy. Other targets such as CD38, CD24, SLAMF7, CD138, and GPRC5D were also found to be expressed in plasma cells of the R/R-MM patient at relapse after BCMA CAR-T cell therapy. Furthermore, exhausted T cells, TIGIT+NK cells, interferon-responsive DCs, and interferon-responsive neutrophils, increased in the R/R-MM patient at relapse after BCMA CAR-T cell treatment. Significantly, the proportion of IL1βhi Mφ, S100A9hi Mφ, interferon-responsive Mφ, CD16hi Mφ, MARCO hi Mφ, and S100A11hi Mφ significantly increased in the R/R-MM patient at relapse after BCMA CAR-T cell therapy. Cell–cell communication analysis indicated that monocytes/macrophages, especially the MIF and APRIL signaling pathway are key players in R/R-MM patient at relapse after BCMA CAR-T cell therapy. Conclusion Taken together, our data extend the understanding of intrinsic and extrinsic relapse of BCMA CAR-T treatment in R/R-MM patient and the potential mechanisms involved in the alterations of antigens and the induced immunosuppressive microenvironment, which may provide a basis for the optimization of BCMA CAR-T strategies. Further studies should be performed to confirm these findings.

Salvage therapies including retreatment with BCMA-directed approaches after BCMA CAR-T relapses for multiple myeloma

“…Although loss of BCMA has been described, 15 , 16 , 17 the majority of patients with relapsed disease after BCMA-directed CAR-T continue to have positive BCMA expression on MM cells, and other factors including CAR-T persistence, T-cell exhaustion, anti-CAR Abs, and the tumor microenvironment may be important determinants of disease relapse. 18 , 19 , 20 Given that BCMA expression is still present in the majority of relapses, 18 retreatment with BCMA-targeted therapies may be a feasible strategy after BCMA-directed CAR-T relapse. In the MajesTEC-1 trial, an ORR of 45% was observed for teclistamab in patients who had prior BCMA-directed CAR-T, with the observed baseline BCMA expression on relapse after CAR-T being comparable with that observed in patients naïve to BCMA treatment on the trial.…”

Innovative prognostic modeling in ESCC: leveraging scRNA-seq and bulk-RNA for dendritic cell heterogeneity analysis

“…In the scRNA-seq analysis, we first utilized the hg38 reference genome and employed the default parameters of Cell Ranger v.7.1.0 software for gene alignment ( 18 ). Following this, we conducted standard single-cell RNA sequencing data analysis using the ‘Seurat’ package in R. After filtering out cells with mitochondrial gene percentage (pMT) over 20%, hemoglobin gene percentage (pHB) over 1%, and those expressing fewer than 500 genes, while retaining genes expressed in at least five cells, we successfully obtained 91,810 high-quality cell samples.…”

Checkpoint CD24 function on tumor and immunotherapy

“…This treatment has also been effective in CD24 subclone-bearing tumors, suggesting that targeting pancreatic cancer stem cells with this method could be a feasible therapeutic strategy for pancreatic cancer. Bispecific BCMA-CD24 CAR-T cells have shown almost complete tumor clearance ability against multiple myeloma cells in vitro and in vivo ( 80 ). However, the antibody used by CD24 CAR-T cells was mouse scFv SWA11, which may cause allergic reactions.…”