Time-series RNA-Seq and data-driven network inference unveil dynamics of cell activation, survival and crosstalk in Chronic Lymphocytic Leukaemia in vitro models

How do cancer cells respond to their environment, and what are the key regulators behind their behaviour? While immune cell reprogramming in the tumour microenvironment (TME) has been extensively studied, the dynamic regulatory changes within cancer cells in response to interactions with immune cells remain poorly understood. In Chronic Lymphocytic Leukaemia (CLL), this knowledge gap limits our ability to fully grasp the disease progression and to design effective, personalised interventions. To tackle this, we combine time-series transcriptomics with data-driven gene regulatory network (GRN) inference to uncover the temporal regulatory mechanisms driving CLL cell behaviour within a reconstituted in vitro TME. Using cultures of peripheral blood from CLL patients or of purified patient-derived CLL cells, we profile gene expression across five time points spanning 14 days under these experimental conditions. By inferring GRNs from transcription factor activity, we capture patient-specific and temporally resolved regulatory interactions that highlight how immune signals shape cancer cell phenotypic changes. Our network analysis reveals distinct gene modules associated with critical processes such as cytokine signalling, metabolic reprogramming and differentiation, hallmarks of immune-cancer cell interaction. Intriguingly, we found that while the presence of immune cells in the environment significantly alters CLL cell activation, their survival trajectories are predominantly governed by intrinsic features. This study not only offers mechanistic insights into how immune cell presence influences CLL cell fate but also presents a robust computational framework for integrating time-series transcriptomics with GRN inference, which can then be used to study the long-term behaviour of the CLL cells through dynamical modelling.