Fig. 4: Intercellular differences in ecDNA content drive gene expression differences.
From: Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells
a, Schematic representation of the three independent ecDNAs identified in TR14: MYCN ecDNA (yellow); CDK4 ecDNA (blue); and MDM2 ecDNA (red). b, UpSet plot displaying the co-occurrence of the three ecDNAs identified in TR14 (MDM2, CDK4, MYCN) in single cells (n = 25 TR14 cells). c, Genome tracks with read densities (log-scaled) over reconstructed ecDNA regions in three exemplary TR14 cells showing different ecDNAs detected. d, Violin plots of mRNA expression levels in TR14 and CHP-212 single cells (two-sided Welch’s t-test; P = 0.0038 (MYCN), P < 2.2 × 10−16 (LPIN1, TRIB2, CDK4, MDM2, MYT1L)); n = 171 CHP-212 cells, n = 42 TR14 cells. e, f, Pairwise comparison between ecDNA and mRNA read counts from scEC&T-seq over the reconstructed MYCN ecDNA region in CHP-212 single cells (two-sided Pearson correlation, P < 2.2 × 10−16, R = 0.86, n = 150 cells) (e) and in TR14 single cells (two-sided Pearson correlation, P = 0.0056, R = 0.54, n = 25 cells) (f). g, h, Pairwise comparison between ecDNA and mRNA read counts from scEC&T-seq over the reconstructed CDK4 (g) and MDM2 (h) ecDNAs in TR14 single cells (two-sided Pearson correlation, P = 0.0046, R = 0.55 for CDK4 and P = 0.0019, R = 0.59 for MDM2, n = 25 TR14 cells).
