Single-Cell Analysis of Anti-BCMA CAR-T Cell Therapy in Patients with Central Nervous System Autoimmune Diseases

Introduction

Chimeric Antigen Receptor (CAR) T-cell therapy has shown potential long-term control in treating central nervous system (CNS) autoimmune diseases. This paper investigates the effects of anti-BCMA (B-cell maturation antigen) CAR-T cells in treating neuromyelitis optica spectrum disorder (NMOSD). NMOSD is an inflammatory autoimmune demyelinating disease of the CNS characterized by recurrent optic neuritis and myelitis, leading to severe neurological dysfunction. Current NMOSD treatment methods fail to effectively target immune dysregulation within the CNS.

CAR-T cell therapy has shown significant potential in treating hematological cancers, but its efficacy and molecular mechanisms in autoimmune diseases remain unclear. This study utilizes single-cell multi-omics sequencing to investigate the characteristics and immune changes in five NMOSD patients who received anti-BCMA CAR-T cell therapy.

Research Source

This study was conducted by a series of scholars including Chuan Qin, Min Zhang, Da-Peng Mou, and others, with major research institutions including Huazhong University of Science and Technology’s Tongji Medical College, Beijing Tongren Hospital, Nanjing IASO Biotechnology Co., Ltd., and others. The research was published in Science Immunology on May 10, 2024.

Research Process

Workflow Details

a) Research Process: - Initial Immune Cell Analysis: The study collected peripheral blood mononuclear cells (PBMCs) and cerebrospinal fluid (CSF) from five anti-AQP4 IgG-positive, refractory/relapsing NMOSD patients and five age- and gender-matched controls for single-cell transcriptomic, T-cell receptor (TCR), and B-cell receptor (BCR) data generation. A total of 113,766 immune cells’ single-cell transcriptome data were obtained. - CAR-T Cell Therapy and Single-Cell Multi-omics Sequencing: Longitudinal blood and CSF samples were collected from the five NMOSD patients who received anti-BCMA CAR-T cell therapy to perform single-cell multi-omics analysis, studying the in-vivo dynamics of CAR-T cells and corresponding changes in the immune system.

b) Main Results: - Immune Cell Changes: Analysis showed abnormal expansion of B-cell lineages, especially plasmablasts and plasma cells, in the blood and CSF of anti-AQP4 IgG-positive NMOSD patients. - CAR-T Cell Dynamics: Flow cytometry and single-cell TCR sequencing revealed that anti-BCMA CAR-T cells peaked at approximately 10 days post-injection and then significantly decreased within a month. CAR-T cells expressed high levels of proliferative and inflammatory genes and exhibited myeloid characteristics at later stages.

c) Research Conclusion and Value: - At various time points post-CAR-T cell injection, the dominant cells were proliferative CD8+ effector T cells with suppressive cytotoxic phenotypes. Anti-BCMA CAR-T cells displayed characteristics distinct from those observed in hematological malignancies. - Enhanced chemotaxis of CAR-T cells facilitated their traversal across the blood-brain barrier, eliminating plasmablasts and plasma cells in the CSF, thereby reducing neuroinflammation. - Studies on CAR-T cell persistence indicated that high expression of CD44 might be associated with the persistence of CAR-T cells in vivo, providing new insights for future therapy optimization.

Research Details

Experiment Design and Data Analysis

Blood and CSF samples were collected from five recurrent anti-AQP4 IgG-positive NMOSD patients and five age-, gender-matched controls. Single-cell transcriptomic sequencing established the transcriptome data of 113,766 immune cells. Simultaneously, paired analysis of TCR and BCR sequences was conducted, and single-cell multi-omics sequencing was used to assess CAR-T cell dynamics at different treatment time points.

Result Analysis

1. B-cell Expansion: In NMOSD patients’ CSF and blood, significant expansion of B-cells, especially plasmablasts and plasma cells, was observed. Single-cell sequencing and paired analysis identified that B-cell clones in the CSF mainly originated from CNS-specific sites rather than circulating precursor cells.

2. Effect of CAR-T Cell Therapy: Post-CAR-T cell therapy, a significant reduction of plasmablasts and plasma cells in the CSF was found, indicating effective traversal of CAR-T cells across the blood-brain barrier and their action within the CSF. Post-injection CAR-T cells exhibited high expression of chemotaxis genes, possibly facilitating their effective traversal and clearance of abnormal cells in the CSF.

3. Persistence of CAR-T Cells: Analysis indicated that high CD44 expression in CAR-T cells was related to their persistence in vivo, while low Sell gene expression suggested a short-lived effector cell nature. Gene enrichment analysis highlighted significant activity in oxidative phosphorylation (oxphos) and granzyme A signaling pathways in long-persistent CAR-T cells.

Main Conclusion

The study results suggest that anti-BCMA CAR-T cell therapy can alleviate neuroinflammation in NMOSD patients, addressing inadequacies in current treatment methods. This therapy effectively crosses the blood-brain barrier, eliminates pathological B-cells in the CSF, and modulates the immune system to achieve therapeutic effects. Additionally, an inhibitory cytotoxic phenotype unique to NMOSD was identified, which may need targeted cell design optimization.

Research Highlights

• Chemotaxis: Enhanced chemotaxis in CAR-T cells enables efficient traversal of the blood-brain barrier, a novel finding of this study.
• CAR-T Cell Persistence: High expression of CD44 and low expression of Sell suggest that future strategies could focus on regulating these markers to enhance CAR-T cell persistence.
• Clinical Significance: The results demonstrate the potential of CAR-T cells in treating refractory CNS autoimmune diseases, proposing new therapeutic strategies.

This study elucidates the mechanism of anti-BCMA CAR-T cell therapy in treating neuromyelitis optica spectrum disorder and provides important new insights for future CAR-T cell treatment plans.