Tumor clone dynamics in gastro-esophageal cancer organoids reveal a non-genetic memory of neoadjuvant chemotherapy via downregulation of NFκB signaling

Adenocarcinomas of the gastroesophageal junction exhibit genetic and non-genetic heterogeneity that impact clinical outcomes, though the underlying mechanisms behind drug resistance remain poorly understood. We integrated bulk whole-genome sequencing (WGS) and single cell RNA sequencing (scRNA-seq) data from patient-derived organoid lines generated from drug resistant gastric tumors of three patients before and after chemotherapy with FLOT (5-fluorouracil, leucovorin, oxaliplatin, and docetaxel), investigating both in vivo and ex vivo treatment effects. We found that inter-patient variability of gene expression exceeds intra-patient differences and predominantly shapes the expression profiles. Integration of WGS-inferred cancer phylogenies with scRNA-seq data allowed us to associate genetic clones with the individual cells’ transcriptional program and to track the genetic and transcriptomic history of dominant genetic clones in post-treatment samples relative to the corresponding primary tumor. Notably, in vivo treated samples appeared to be transcriptionally distinct from the untreated counterparts, marked by sustained NF-κB down-regulation, which suggests that they retain an immune-mediated imprint of the prior therapy. Changes in the clonal composition of a tumor alone cannot explain the post-chemotherapy NF-κB-associated transcriptional reprogramming. Instead, non-genetic mechanisms shape the altered transcriptomic landscape, particularly a distinct subpopulation of epithelial cells that specifically express pro-inflammatory cytokines, key components of the NF-κB regulatory network. These observations support a model of transcriptional reprogramming after FLOT treatment, which is most likely independent of genetic evolution and consequently potentially reversible. Downregulated NF-κB signaling may thus represent a candidate pathway change for predictive response assessment and/or NF-κB-stimulating co-therapeutic strategies to overcome FLOT resistance.