Extended Data Fig. 7: Model for ER-induced R-loops in ecDNA genesis.

a) Simplified schematic illustrating model. Blue letters correspond to figure panels in Extended Data Fig. 7. Created with BioRender.com. b) Number of translocations in cyclic vs. non-cyclic amplifications across subgroups. Boxplot represents median, 0.25 and 0.75 quantiles with whiskers at 1.5x interquartile range. c) ESR1 mRNA abundance in cyclic amplification-positive vs. -negative (top) and non-cyclic amplification-positive vs. -negative (bottom) primary from Nik-Zainal et al., TCGA or metastatic tumors stratified by the IC subgroups, considering ER+ High-risk and HER2+ subgroups. Odds ratio from logistic regression correcting for tumor purity and error bars represent 95% confidence intervals. d) Density of APOBEC3B and ER ChIP-Seq peaks within cyclic and complex non-cyclic amplifications in primary tumours. e) ER early signaling transcriptional signature in DCIS and primary ER+ Typical vs. ER+ High-risk tumors. f-g) Density of ER-induced R-loops in cyclic and complex non-cyclic amplifications stratified by IC subgroups in primary (f) and metastatic (g) tumours. h) Density of all R-loops in cyclic vs. non-cyclic amplifications in primary and metastatic tumors. i) Difference in number of R-loops between A3B knockout (KO) wildtype (WT) MCF10A cell lines overlapping cyclic or non-cyclic amplifications at baseline or after A3B activation (PMA treatment). j-k) Median distance between a translocation and its closest ER-induced R-loop considering translocations within or outside cyclic amplifications in primary (j) and metastatic (k) tumors. l) Percent of breakpoints that overlap any R-loop with (+) or without (−) E2 treatment. Error bars represent the standard deviation across three replicates. m) Proportion of samples with or without ecDNA stratified by inferred APOBEC3B germline copy number. The total number of samples is included at the top of each bar. In b and j-l fold change (FC) and p-values or false discovery rates (FDR) are from Mann-Whitney Rank Sum test. In d-i, effect sizes (ES) are the difference in medians and p-values are from Mann-Whitney Rank Sum test. BER, base-excision repair; TC-NER, transcription-coupled nucleotide excision repair; E2, estrogen.