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

Wei Li; Binglei Zhang; Weijie Cao; Wenli Zhang; Tiandong Li; Lina Liu; LinPing Xu; Fengcai Gao; Yanmei Wang; Fang Wang; Haizhou Xing; Zhongxing Jiang; Jianxiang Shi; Zhilei Bian; Yongping Song

doi:10.1186/s40164-023-00402-5

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

Exp Hematol Oncol. 2023 May 8;12(1):44. doi: 10.1186/s40164-023-00402-5.

Authors

Wei Li^#^{1

2}, Binglei Zhang^#^{1

2}, Weijie Cao^#^{1

2}, Wenli Zhang^{1

2

3}, Tiandong Li⁴, Lina Liu³, LinPing Xu⁵, Fengcai Gao^{1

2}, Yanmei Wang⁶, Fang Wang^{1

2}, Haizhou Xing^{1

2}, Zhongxing Jiang^{1

2}, Jianxiang Shi⁷, Zhilei Bian^{8

9}, Yongping Song^{10

11}

Affiliations

¹ Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
² Department of Hematology, Henan Provincial Hematology Hospital, Zhengzhou, 450000, Henan, China.
³ Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, Henan, China.
⁴ College of Public Health, Zhengzhou University, Zhengzhou, 450000, Henan, China.
⁵ Department of Research and Foreign Affairs, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450008, China.
⁶ Department of Hematology, Zhengzhou People's Hospital, Zhengzhou, 450003, Henan, China.
⁷ BGI College & Henan Institute of Medical and Pharmaceutical Sciences in Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, Henan, China. jianxiangshi@zzu.edu.cn.
⁸ Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China. bianzhilei@zzu.edu.cn.
⁹ Department of Hematology, Henan Provincial Hematology Hospital, Zhengzhou, 450000, Henan, China. bianzhilei@zzu.edu.cn.
¹⁰ Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China. songyp@zzu.edu.cn.
¹¹ Department of Hematology, Henan Provincial Hematology Hospital, Zhengzhou, 450000, Henan, China. songyp@zzu.edu.cn.

^# Contributed equally.

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 IL1β^hi Mφ, S100A9^hi Mφ, interferon-responsive Mφ, CD16^hi Mφ, MARCO ^hi Mφ, and S100A11^hi 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.

Keywords: BCMA CAR-T; Monocyte/macrophages; Multiple myeloma; Resistant mechanisms; ScRNA-seq; T cell exhaustion.

Abstract

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