Figure 2 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Authors: Rosano Dalia , Sofyali Emre , Dhiman Heena , Ghirardi Chiara , Ivanoiu Diana , Heide Timon , Vingiani Andrea , Bertolotti Alessia , Pruneri Giancarlo , Canale Eleonora , Dewhurst Hannah F. , Saha Debjani , Slaven Neil , Barozzi Iros , Li Tong , Zemlyanskiy Grigory , Phillips Henry , James Chela , Győrffy Balázs , Lynn Claire , Cresswell George D. , Rehman Farah , Noberini Roberta , Bonaldi Tiziana , Sottoriva Andrea , Magnani Luca 
Published: May 2024

<p>TRADITIOM genetic analysis and lineage composition. <b>A,</b> Cell counts for MCF7 and T47D HYPERflasks for −E2 (circle) and TAM (diamond) arms at their respective time of collection (teal: latency–time between the onset of the treatment and cell cycle arrest in the whole cell population; yellow: dormancy, magenta: awakening, early progression. α−ζ: MCF7 awakening carbon copies, <b>A–F</b>: T47D awakening carbon copies). <b>B,</b> TRADITIOM Live set-up: 12 replicates were seeded in a 48-well plate and imaged two times a week for 150 days using Incucyte Zoom (9 scanning windows per well) to monitor awakening dynamics. Awakening was defined as wells reaching a confluency of 50%. Minor differences in initial plating (violin plot) do not predict awakening times. <b>C,</b> Heatmap of MCF7 high-frequency barcodes (frequency ≥10%) among UT (untreated) samples’ endpoints and TRADITIOM carbon copies (replicates) for both TAM and –E2 arm (AI) at the time of dormancy and awakening (T30–60, AI30–60: dormancy time points, cells treated for 30 or 60 days with tamoxifen or estrogen deprivation, respectively). <b>D,</b> Phylogenetic tree for MCF7 TRADITIOM samples based on SNVs and indels (VAF >10%). Data depict TRADITIOM samples from POT (pretreatment), awakenings (early progression), and TEPs (late progression) of both treatment arms [TAM and AI (–E2)] and their untreated counterpart samples (UT) cultured in parallel for 170 days. <b>E,</b> VAF heatmap for ET resistance driver genes in ER<sup>+</sup> breast cancer, compiled based on Bertucci et al. (<a href="#bib14" target="_blank">14</a>) derived from TRADITIOM WGS, illustrating only variants with significant changes in VAF across samples (Fisher exact test, <i>P</i> < 0.01). <b>F,</b> Heatmap of T47D high frequency barcodes (frequency ≥10%) among UT (untreated) samples’ endpoints and TRADITIOM carbon copies (replicates) for –E2 (AI) arm at the time of dormancy and awakening. <b>G,</b> Phylogenetic tree for T47D TRADITIOM samples based on SNVs and indels (derived from the targeted sequencing using a custom targeted panel, VAF >10%). <b>H,</b> VAF heatmap for ET resistance driver genes in ER<sup>+</sup> breast cancer, compiled based on Bertucci et al. (<a href="#bib14" target="_blank">14</a>) derived from the targeted sequencing using a custom targeted panel, illustrating only variants with significant changes in VAF across samples (Fisher exact test, <i>P</i> < 0.01). Data depict T47D TRADITIOM samples from POT (pretreatment), awakenings (early progression), and TEPs (late progression) of both treatment arms (TAM and –E2) and their counterpart untreated (UT) samples cultured in parallel for 180 days.</p>