Datasets and Rscripts for : Multiomic Dissection of Movement and Neurocognitive Toxicity Following BCMA-Targeting CAR T Cell Therapy

Seurat Objects

ds_indexContains all cells recovered via scRNA-seq and scTCR-seq from cerebrospinal fluid (CSF) and peripheral blood mononuclear cells (PBMCs) of an index patient who developed parkinsonism following CAR-T cell therapy. Samples were collected longitudinally across multiple time points (day 20 to day 204 post–CAR T).

T_cells_indexSubset of ds_index comprising T cells identified from the combined CSF and PBMC samples of the index patient (day 20 to day 204 post–CAR-T).

ds_controlContains all cells recovered from peripheral blood (PBMCs) via scRNA-seq and scTCR-seq from:

the index patient at early time points (pre–CAR-T and day 7 post–CAR-T), and

three additional control patients treated with cilta-cel, sampled at matched time points (pre–CAR-T and day 9/10 post–CAR-T).

T_cells_controlSubset of ds_control comprising T cells identified from PBMC samples of the index patient (pre–CAR-T and day 7 post–CAR-T) and the three control patients treated with cilta-cel (pre–CAR-T and day 9/10 post–CAR-T).

R Scripts

Additionally, three R scripts are provided:

Index patient preprocessing scriptDetails the quality control, normalization, integration, and annotation steps applied to the index patient datasets.

Index patient downstream analysis and visualization scriptContains the code used to generate figures and perform downstream analyses for the index patient, including clonal and phenotypic characterization.

Early time point and control cohort processing scriptDescribes the quality control, Seurat object creation, and visualization steps for early time point samples (ds_control and T_cells_control) from the index patient and control cohort.