Extended Data Fig. 6: T and B cell clonal dynamics of TLS.

a, Representative images showing method of identification and microdissection of individual TLS. Image on left shows HCC tumor stained with hematoxylin and eosin (H&E) at low magnification. Insets show higher magnification of staining with H&E, anti-CD20 (magenta) and anti-Ki67 (brown), anti-CD3 (magenta) and anti-CD21 (brown), anti-CD4 and anti-CD8 (bottom right), and corresponding pre- and post-microdissection images. Scale bar, 1 mm. b-c, Total number of T cell receptor beta chain (TCRβ) (b) and immunoglobulin heavy chain (IGH) (c) clones identified in microdissected TLS. d, Box-and-whisker plot comparing the percentage of the TCRβ or IGH repertoire of each TLS that is shared with other TLS from the same tumor, by ___location. e-f, Dotplots showing TCRβ (e) and IGH (f) repertoire clonality (as determined by Normalized Shannon Entropy) for matched mature and involuted TLS. g, Violin plots comparing number of IGH V gene substitutions in mature and involuted TLS, by patient. Individual data points (not shown) represent individual IGH sequences. Statistical significance was determined by one-way ANOVA followed by Tukey’s honest significant difference (HSD) test (d) and two-tailed t test (e-g). For each box-and-whisker plot, the horizontal bar indicates the median, the upper and lower limits of the boxes the interquartile range, and the ends of the whiskers 1.5 times the interquartile range. For each violin plot, the horizontal bar indicates the median and the upper and lower limits of the boxes the interquartile range.