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Single-cell multi-omics profiling of PBMCs from SLE patients pre- and post-dual-target (BCMA/CD19) CAR-T therapy

ABSTRACT: We employed single-cell RNA sequencing combined with BCR/TCR profiling to study PBMCs from 5 SLE patients before treatment and after peripheral B-cell reconstitution following dual-target (BCMA/CD19) CAR-T therapy. PBMCs were analyzed to characterize dynamic immune cell subsets, BCR/TCR clonal expansion, and SLE-related pathways. This study provides a single-cell landscape of dual-target CAR-T therapy in SLE, offering insights into efficacy and potential biomarkers.

ORGANISM(S): Homo sapiens

PROVIDER: GSE304878 | GEO | 2025/08/08

REPOSITORIES: GEO

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Project description:Multiple myeloma (MM) immune escape resulting from B cell maturation antigen (BCMA) target loss is considered to be a rare event that mediates MM resistance to anti-BCMA chimeric antigen receptor T cell (CAR T) or bispecific T cell engager (TCE) therapies. Emerging clinical data also suggests that downregulation of G protein coupled receptor family C group 5 member D (GPRC5D), another promising target antigen expressed on MM cells, is observed in patients at relapse post anti-GPRC5D CAR T, but the genomic mechanisms that underlie GPRC5D loss has not been described. In order to examine the tumor intrinsic factors that promote MM antigen escape, we performed combined bulk whole genome sequencing and single cell copy number variation analysis on CD138+ cells from bone marrow aspirates of patients before and after relapse from anti-BCMA or -GPRC5D CAR T/ TCE. We describe five cases with distinct biallelic events on TNFRSF17 at MM relapse after CAR T/ TCE. In addition to focal biallelic deletions at the TNFRSF17 locus acquired at relapse, BCMA negative clones can emerge from the selective expansion of subclones with homozygous TNFRSF17 loss that exist prior to any anti-BCMA therapy exposure. Furthermore, we corroborate with functional data to demonstrate that three different non-truncating mutations in the extracellular domain of BCMA negates the efficacies of BCMA directed TCEs and mediate disease relapse in patients. With respect to GPRC5D, we report four cases of MM relapse with biallelic loss of GPRC5D following anti-GPRC5DxCD3ε. Our data support that immunoselection of BCMA negative or mutant clones post anti-BCMA therapies may be more frequent than currently accepted in the field, and that an all or none screening approach for BCMA expression is inadequate to detect pertinent mutations that affect patient response to targeted therapies. We also highlight the importance of developing immunotherapies targeting novel and non-redundant epitopes or antigens in MM

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Single-cell multi-omics profiling of PBMCs from SLE patients pre- and post-dual-target (BCMA/CD19) CAR-T therapy

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