Extended Data Fig. 6: snRNA sequence based analysis of the brain of CAR-T-cell treated mice.

(a) Heat map depicting top genes (rows) enriched per cell type from the CNS of indicated groups. Colors in the heat map correspond to scaled expression. (b) The Dot plot shows marker gene expression of selected genes in cells from the CNS of B-NHL (A20) bearing mice treated with NT compared to CD19-CAR T-cells. (c) UMAP visualization of microglia from the CNS of B-NHL-bearing mice treated with NT-T-cells compared to CD19-CAR-T-cells. Color-coding is based on cluster assignment into 7 clusters. A total of 5,110 cells were included in the UMAP. (d) Marimekko plot showing frequency of microglia derived from the indicated groups across 7 clusters. (e) Dot plot for gene ontology (GO) terms associated with each cluster of microglia. Size and color of the dots correspond to gene ratio and adjusted p-value respectively. (f) Volcano plot showing the differentially expressed genes in microglia from the indicated groups. The –log10-transformed adjusted P value (P-adj, y-axis) is plotted against the log2-transformed fold change in expression between the two treatment groups (x-axis). (g) The violin plot shows the number of genes detected per nucleus of cells from the CNS of the indicated groups. (h-j) The scatter plot shows neurocognitive assessment of non-tumor-bearing C57BL/6 mice treated with NT (mice, n = 5), or CD19-CAR (mice, n = 5) T-cells. Time spent exploring the novel object (h), Time spent in safe zone (i). Neurophenotypic scores from day1-5 post T-cell transfer (j). (k-p) Immunofluorescence imaging representing the NeuN⁺, DAPI⁺ cells from the Cortex (k, l, m and o) or hippocampus (n and p) from the CNS of B-NHL or B-ALL-bearing mice treated with either PBS (mice, n = 4-9), NT (mice, n = 4-10) or CD19 CAR (mice, n = 4-8). (k, m, n) Representative images (k) (Scale bar: 100 µm), (m, n) (Scale bar: 400 µm), (l, o, p) quantification. The experiment or staining was performed once (a-j, m-p), twice (k, l) and the results (mean ± s.e.m) were plotted. P-values were calculated using two-tailed students unpaired students t-test (h, i). P-values were calculated using one-way ANOVA (l) with mixed effect analysis (j) or Kruskal-Wallis test (o, p).