Mapping drug-microenvironment-genetic interplay in CLL reveals trisomy 12 as a modulator of microenvironmental signals

The tumour microenvironment and gene mutations collectively influence drug efficacy in Chronic Lymphocytic Leukaemia (CLL), however an integrative understanding of their interplay is missing. We performed a combinatorial assay using 12 drugs individually co-applied with each of 17 microenvironmental stimuli in 192 primary CLL samples, generating a comprehensive map of drug-microenvironment interactions in CLL. We combined our data with whole-exome sequencing, DNA-methylation, RNA-sequencing and copy number variant data. We complemented these experiments by staining healthy and CLL-infiltrated lymph nodes for downstream mediators of key microenvironmental pathways. Our assay identified four distinct CLL subgroups that differed in their responses to the panel of stimuli and in patient outcomes, distinct from known prognostic groups. Additionally, we identified trisomy 12 as an amplifier of responses to the stimuli, mediated by the transcription factors Spi-B and PU.1. We quantified the impact of the stimuli on drug response, distinguished antagonistic and synergistic combinations and characterised their dependency on genetic alterations. The most frequent modulators of drug responses were stimuli activating Interleukin (IL) 4 and Toll-Like Receptor 7/8/9 signaling. Both pathways were more active in CLL-infiltrated lymph nodes than in healthy samples (p<0.001), and high IL4 activity in lymph nodes correlated with shorter survival (p=0.038). We provide a publically-available resource to investigate microenvironmental, genetic and drug interplay in CLL. Our results highlight the importance of tumour cell extrinsic influences on drug response and disease progression, and how these are further modulated by cell intrinsic molecular features.The tumour microenvironment has distinct effects in patient subgroups and modulates drug sensitivity and CLL proliferative capacity.Systematic dataset identifies trisomy 12 and JAK-STAT signalling as important players in cell-extrinsic drug resistance mechanisms.