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Figure 6 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells

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posted on 2024-05-01, 07:42 authored by Dalia Rosano, Emre Sofyali, Heena Dhiman, Chiara Ghirardi, Diana Ivanoiu, Timon Heide, Andrea Vingiani, Alessia Bertolotti, Giancarlo Pruneri, Eleonora Canale, Hannah F. Dewhurst, Debjani Saha, Neil Slaven, Iros Barozzi, Tong Li, Grigory Zemlyanskiy, Henry Phillips, Chela James, Balázs Győrffy, Claire Lynn, George D. Cresswell, Farah Rehman, Roberta Noberini, Tiziana Bonaldi, Andrea Sottoriva, Luca Magnani

Targeting the dormant epigenome. A, Clustered heat maps of histone posttranslational modifications of super-SILAC mass spectrometry for TRADITIOM MCF7 and T47D samples [time zero (T0), latency (time between treatment onset and dormancy entry), dormancy, awakening (early progression), and TEPs (late progression)]. Significantly enriched (dormancy 30 days vs. TEPs, two-tailed t test: *, P < 0.01; **, P < 0.001; ***, P < 0.0001) modifications are depicted in bold, and the ones found to be associated with dormancy are highlighted in yellow. B, Schematic representation of small-molecule inhibitor experiments. Inhibitors against G9a (H3K9me2), EZH2 (H3K27me3), and KMT5B/C (H4K20me3) were used either alone or in combination. Start time of the inhibition was either at the beginning of estrogen deprivation to target persister pool generation or at 30 days of estrogen deprivation (dormancy) to target established dormant cells. C, Proliferation dynamics of MCF7 cells in E2-supplemented conditions (+E2) after treatment with inhibitors against EHMT2, EZH2, KMT5B/C, dual combinations of each and vehicle. D, Proliferation dynamics of MCF7 cells in estrogen-deprived conditions (−E2) after treatment with inhibitors against G9a, EZH2, KMT5B/C, dual combinations of each and vehicle. Proliferation dynamics of T47D cells in E2-supplemented (+E2; E) and deprived (−E2) conditions (F) after treatment with inhibitors against G9a, EZH2, KMT5B/C, dual combinations of each and vehicle (one-way ANOVA with Dunnett correction: *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001). Error bars represent standard deviation (n = 3). G, Relapse-free survival (RFS) curves for ER+ breast cancer patients stratified based on the expression of the epigenetic dormancy signature (high vs. low EHMT2/EZH2/KMT5C expression). Left: no adjuvant treatment; middle: adjuvant endocrine therapy (TAM/AI); right: AI adjuvant treatment. Multivariate analysis for clinically relevant prognostic biomarkers is shown in the onset table. H, Proliferation dynamics of MCF7 dormant cells (pretreated for 30 days with –E2) after treatment with inhibitors against G9a, EZH2, KMT5B/C, dual combinations of each and vehicle (one-way ANOVA with Dunnett correction: *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001). Error bars represent standard deviation (n = 3). I, Model: endocrine therapy-induced dormancy is characterized by a consistent epigenetic reprogramming involving a global increase in histone repressive marks (H3K9me2, H3K27me3, and H4K20me3). The dormant epigenome is unstable and through a progressive loss of the histone repressive marks (erosion), cells resume proliferation in a process that mimics patient relapse (awakening). Epidrugs (G9a/EZH2/KMT5B/C inhibitors) can interfere with epigenetic reprogramming and block the formation of persister dormant clones. During adaptation, dormant cells engage in sporadic cycling (failed awakening) while under therapeutic stress possibly forcing cells into a subsequent round of epigenetic reprogramming that could also be antagonized with epidrugs.

Funding

Cancer Research UK (CRUK)

Horizon 2020 Framework Programme (H2020)

History

ARTICLE ABSTRACT

Patients with estrogen receptor–positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs. This study advances the understanding of therapy-induced dormancy with potential clinical implications for breast cancer. Estrogen receptor-positive breast cancer cells adapt to endocrine treatment by entering a dormant state characterized by strong heterochromatinization with no recurrent genetic changes. Targeting the epigenetic rewiring impairs the adaptation of cancer cells to ETs.See related commentary by Llinas-Bertran et al., p. 704.This article is featured in Selected Articles from This Issue, p. 695