Figure 3.
Exhausted effector T cells in patients with CD20+ relapse from CD20 bispecs. (A) CD79A and CD20 protein expression determined using IHC on FFPE biopsy sections. The images show staining from patient 2 before CD20 bispec treatment (sample 2.1) and at relapse (sample 2.4), demonstrating relapse with retained CD20. (B) Schematic illustration showing the strategy used to compare scRNA-seq T cells from samples obtained during CD20 bispec treatment, including tumor-free or responsive lesions (n = 2, sample 3.3 and 7.1), CD20⁻ relapse (n = 1, sample 3.2) and CD20+ relapse (n = 3; sample 2.4, 2.5, and 7.2). T cells were combined into a joint embedding, and exhaustion was interrogated based on an established exhaustion gene signature within CD8 subpopulations. The exhaustion scores within CD8 effector T cells were compared between patients who experienced CD20+ relapse (patients 2 and 7) and the patient who did not experience CD20+ relapse (patient 3). (C) Joint UMAP embedding of 6381 T cells from 6 samples. T cells are color-coded based on identified subpopulation. (D) Heat map showing T-cell subset and state gene signature scores across subpopulations, underlying the subpopulation annotation in panel C. (E) Cells are color-coded based on their exhaustion signature score, which was computed across CD8 subpopulations. The gene list underlying the exhaustion score can be found in supplemental Table 3. (F) Box plot depicting the exhaustion scores within CD8 effector T cells across samples. Statistical significance was assessed using a pairwise, 2-sided Wilcoxon rank-sum test against combined samples 3.2 and 3.3 (∗∗∗P < 2.22 × 10⁻16). Center line indicates the median, box limits indicate the upper and lower quantiles, and whiskers indicate the 1.5× interquartile range. (G) Bar plot demonstrating proportions of T-cell subpopulations across samples. eff, effector; IFN, interferon; NK, natural killer; NKT, natural killer T cell; Tfh, T follicular helper; Th, T helper; Treg, regulatory T cell; UMAP, uniform manifold approximation and projection.

Exhausted effector T cells in patients with CD20+ relapse from CD20 bispecs. (A) CD79A and CD20 protein expression determined using IHC on FFPE biopsy sections. The images show staining from patient 2 before CD20 bispec treatment (sample 2.1) and at relapse (sample 2.4), demonstrating relapse with retained CD20. (B) Schematic illustration showing the strategy used to compare scRNA-seq T cells from samples obtained during CD20 bispec treatment, including tumor-free or responsive lesions (n = 2, sample 3.3 and 7.1), CD20⁻ relapse (n = 1, sample 3.2) and CD20+ relapse (n = 3; sample 2.4, 2.5, and 7.2). T cells were combined into a joint embedding, and exhaustion was interrogated based on an established exhaustion gene signature within CD8 subpopulations. The exhaustion scores within CD8 effector T cells were compared between patients who experienced CD20+ relapse (patients 2 and 7) and the patient who did not experience CD20+ relapse (patient 3). (C) Joint UMAP embedding of 6381 T cells from 6 samples. T cells are color-coded based on identified subpopulation. (D) Heat map showing T-cell subset and state gene signature scores across subpopulations, underlying the subpopulation annotation in panel C. (E) Cells are color-coded based on their exhaustion signature score, which was computed across CD8 subpopulations. The gene list underlying the exhaustion score can be found in supplemental Table 3. (F) Box plot depicting the exhaustion scores within CD8 effector T cells across samples. Statistical significance was assessed using a pairwise, 2-sided Wilcoxon rank-sum test against combined samples 3.2 and 3.3 (∗∗∗P < 2.22 × 10⁻16). Center line indicates the median, box limits indicate the upper and lower quantiles, and whiskers indicate the 1.5× interquartile range. (G) Bar plot demonstrating proportions of T-cell subpopulations across samples. eff, effector; IFN, interferon; NK, natural killer; NKT, natural killer T cell; Tfh, T follicular helper; Th, T helper; Treg, regulatory T cell; UMAP, uniform manifold approximation and projection.

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