Cellular adaptation to cancer therapy along a resistance continuum [ATAC-seq: Kuramochi]

Advancements in precision oncology over the past decades have led to new therapeutic interventions, but the efficacy of such treatments is generally limited by an adaptive process that fosters drug resistance. In addition to genetic mutations, recent research has identified a role for non-genetic plasticity in transient drug tolerance and the acquisition of stable resistance. However, the dynamics of cell-state transitions that occur in the adaptation to cancer therapies remain unknown and require a systems-level longitudinal framework. Here we demonstrate that resistance develops through trajectories of cell-state transitions accompanied by a progressive increase in cell fitness, which we denote as the 'resistance continuum'. This cellular adaptation involves a stepwise assembly of gene expression programmes and epigenetically reinforced cell states underpinned by phenotypic plasticity, adaptation to stress and metabolic reprogramming. Our results support the notion that epithelial-to-mesenchymal transition or stemness programmes-often considered a proxy for phenotypic plasticity-enable adaptation, rather than a full resistance mechanism. Through systematic genetic perturbations, we identify the acquisition of metabolic dependencies, exposing vulnerabilities that can potentially be exploited therapeutically. The concept of the resistance continuum highlights the dynamic nature of cellular adaptation and calls for complementary therapies directed at the mechanisms underlying adaptive cell-state transitions. Adapted (olaparib resistant) Kuramochi cell populations to 5 uM (T5), 10 uM (T10), 20 uM (T20), 40 uM (T40), 80 uM (T80), 160 uM (T160) and 320 uM (T320) of olaparib plus untreated controls (C) were sorted based on their CD24/CD44 profiles and ATAC-Seq was performed. Drug-naïve Kuramochi cell populations were treated with olaparib for 9 days with 10 uM (P10) and 320 uM (P320) of olaparib and ATAC-Seq was performed. To evaluate the stability of the chromatin changes, the parental T320 cells were cultured without drug (T320W) for 120 days. Both T320 and T320W were either untreated or re-treated with 320 uM of olaparib for 2 days and ATAC-Seq was performed. Two replicates per condition were generated.