Fig. 3: Changes of cancer state-specific 3D genome features during lung cancer progression.
From: Tracing the evolution of single-cell 3D genomes in Kras-driven cancers
a, Demixing scores (s.d. of normalized mean interloci distances) of the active chrX (Xa, n = 95) and inactive chrX (Xi, n = 95) in human IMR90 cells show a reduction (increased intermixing) in Xi, as previously described using other analyses11. P value from two-sided Levene’s test is shown. b, Distributions of demixing scores of each autosome (n = 19) in each cell state. n = 4,806, 791, 1,603, 1,941 and 17,711 for WT AT2, AdenomaR, AdenomaY, AdenomaG and LUAD cells, respectively. Cell numbers of each cell state are identical in b–i. c, log2(FC) of the demixing score of each autosome, comparing each cancer state to WT AT2 cell state. An asterisk indicates FDR < 0.05, two-sided Levene’s test. d, Distribution of polarization indices of each autosome (n = 19) in each cell state. e, Distribution of interchromosomal distances in each cell state. f, log2(FC) of mean interloci distances for AdenomaR, AdenomaY and AdenomaG relative to AT2 cells. Yellow lines highlight the boundaries of chromosomes. g, Distributions of radial scores of chr13, chr7 and chr19 in each cell state. h, Mean log2(FC) of radial scores of each chromosome, comparing each cancer state to the AT2 cell state. An asterisk indicates FDR < 0.05, two-sided Wilcoxon signed-rank test. i, log2(FC) of mean interloci distances for LUAD relative to AT2 cells. Yellow lines highlight the boundaries of chromosomes. j, Nuclear convex hull volume of WT AT2, AdenomaR, AdenomaY, AdenomaG and LUAD cells. P values of two-sided Wilcoxon rank-sum tests are shown. n = 3,410, 157, 689, 878 and 8,834 for WT AT2, AdenomaR, AdenomaG, AdenomaY and LUAD cells, respectively (cells with at least 10 traces). In b, d, e and g, P values of two-sided Wilcoxon signed-rank test comparing each cancer state to WT AT2 state with matched autosomes (b,d) or matched genomic loci (e,g) are displayed. In b, d, e, g and j, horizontal lines of each box represent the 75th percentile, median and 25th percentile. Whiskers indicate nonoutlier maximum and nonoutlier minimum, with outlier thresholds at 1.5× interquartile range beyond box limits.
