Roux C, Hamer S, Shea A (2023). Environment-Dependent Modes of Adaptive Evolution in Neuroblastoma: Plasticity as a Selectable Trait

The following Zenodo archive details data files used to conduct computational analysis of all components linked to sequencing. Code and scripts associated with this analysis can be found on the following Github Repository: https://github.com/PCEBrunaLab/Roux-et-al.-2024/. Phenotypic heterogeneity is a hallmark of aggressive cancers such as neuroblastoma, fuelling therapeutic resistance and disease progression. However, the role of phenotypic plasticity in shaping tumour heterogeneity and evolution remains poorly defined. Here, we present a multi-resolution quantitative framework to characterise the principles, types, and dynamics of phenotypic plasticity in neuroblastoma at single-cell resolution. Leveraging expressed DNA barcode technology, we simultaneously trace clonal and phenotypic trajectories in evolving tumour populations, enabling precise quantification of plasticity across time and environmental conditions.Building on previous observations, we demonstrate that plasticity in neuroblastoma is a selectable trait. Individual lineages exhibit intrinsic, heritable differences in the magnitude and mode of phenotypic transitions, independent of their initial cell state. Crucially, lineages with high intrinsic transition dynamics are positively selected under treatment, leading to a phenotypically similar, yet plasticity-enhanced post-treatment population. Plasticity enables the awakening and recovery of drug-tolerant persister (DTP) cells, driving irreversible adaptation and the emergence of cell populations with increased proliferative capacity, stem-like features, and reduced treatment sensitivity. Longitudinal multi-omic profiling reveals that this plasticity memory is maintained through chromatin remodelling and increased accessibility of ATF2-dependent transcriptional programmes. Consistently, inhibition of ATF2 disrupts plasticity-driven awakening and impairs adaptive resistance.Our approach underscores the power of integrated clonal and phenotypic lineage tracing with mulitomics to resolve non-genetic evolution in cancer. Together, our findings uncover a novel epigenetically encoded mechanism of phenotypic plasticity memory that promotes the selection and persistence of plastic cell states during tumour evolution, positioning phenotypic plasticity as a central driver of therapeutic escape in neuroblastoma and highlighting new therapeutic opportunities to target non-genetic mechanisms of resistance to improve treatment outcomes in neuroblastoma.