Time-series RNA-seq analysis reveals dynamic transcriptional responses and crosstalk in chronic lymphocytic leukaemia (CLL) autologous and monoculture in vitro models

Chronic lymphocytic leukaemia (CLL) cells were cultured either within autologous peripheral blood mononuclear cells (PBMCs) or as purified monocultures and sampled at five time points (days 1, 4, 8, 11 and 14) to capture dynamic transcriptional programs during ex vivo activation and survival. Time-series RNA-seq was performed on 60 samples derived from three patients (DAR, SAS, PRG), enabling the reconstruction of gene expression trajectories and identification of signalling pathways contributing to CLL activation, immune crosstalk and prolonged viability. Overall design: RNA-seq profiling of autologous PBMC cultures and purified B-CLL cell monocultures from 3 CLL patients over a 14-day time course (days 1, 4, 8, 11, 14).