Extended Data Fig. 6: Spatial distribution of T and B cells and identification of TLSs. | Nature Genetics

Extended Data Fig. 6: Spatial distribution of T and B cells and identification of TLSs.

From: Multi-omic profiling highlights factors associated with resistance to immuno-chemotherapy in non-small-cell lung cancer

Extended Data Fig. 6

a, The spatial distribution of T cells in patient 11 (P11). The darker red color represents a higher cell-type proportion. b, The spatial distribution of B cells P11. The darker red color represents a higher cell-type proportion. c, Boxplots showing the differences in T cell subtype proportions in tumor (n = 150), tumor boundary (n = 162) and stromal (n = 3651) regions in patient P11. Statistical significance was determined by two-sided Wilcoxon rank-sum test. ns: P > = 0.05; *: P < 0.05; **: P < 0.01; ***: P < 0.001; ****: P < 0.0001. d, Heat-dot plot showing cell-type colocalizations in patient P11. Pearson correlations of the estimated cell-type proportions were calculated for each pair of cell types across all spots. The color and size of the dot represent the correlation coefficient. A positive correlation coefficient indicates colocalization of the cell-type pair, whereas negative values indicate exclusion of the two cell types from each other. The black rectangle highlights the colocalization of T and B cells. e, Pathological examination of TLSs in patient P11. Scale bar: 1 mm. All Visium slides (n = 17) were examined. f, The automated TLS identification workflow named Space Scanner through combining H&E image and ST data. g, Location of identified TLSs in patient P11. Red and gray colors represent TLSs and surrounding stroma respectively. h, Heatmap showing the averaged expression of 12 chemokines in TLSs and stroma from patient P11. i, Boxplots showing the differences in B (left panels) and T (right panels) cell subtype proportions within TLSs (n = 210) and stroma (n = 294) in patient P11. Statistical significance was determined by two-sided Wilcoxon rank-sum test. ns: P > = 0.05; *: P < 0.05; **: P < 0.01; ***: P < 0.001; ****: P < 0.0001. For the boxplots in c and i, the box limits denote the first and third quartiles, with the median shown in the center and whiskers covering data within 1.5× the interquartile range from the box.

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