R data package for Single-cell RNA-seq analysis reveals distinct tumor and immunosuppressive T-cell phenotypes in CLL patients treated with ibrutinib.

The development of Bruton tyrosine kinase inhibitors (BTKi) and their introduction into clinical practice represents a major advance in the treatment of chronic lymphocytic leukemia (CLL). However, monotherapy with ibrutinib or other BTKis generally does not induce complete remissions or undetectable minimal residual disease (MRD) even with extended therapy. Therefore, there is a need to understand the differences between ibrutinib sensitive and resistant CLL cells along with the immune microenvironment to identify novel therapeutic approaches for controlling residual disease during BTKi treatment. Here, we investigated the cellular heterogeneity of peripheral blood mononuclear cells from patients with CLL treated with ibrutinib using single-cell RNA sequencing. We identified unique transcriptional heterogeneity within the B cell cluster in the ibrutinib-sensitive and resistant patients. Ibrutinib sensitive cells showed enrichment of B cell populations with upregulation of MHC I molecules and TNF family members. Additionally, we observed that inflammatory response and metabolism related pathways were decreased, whereas cellular response to stress and DNA repair programs were increased in the ibrutinib resistance samples. T cells in ibrutinib-resistant patients showed expansion of Tregs and an exhausted CD8 effector T cell compartment. Furthermore, CD14+ and CD16+ monocytes from ibrutinib resistant patients preferentially expressed a gene expression program of antiviral immunity. At the single-cell level, our findings demonstrate a picture of transcriptional heterogeneity in the tumor compartment and immune milieu. Overall, these findings highlight transcriptional changes in circulating immune cells associated with ibrutinib resistance, suggesting that T cells exhaustion and monocyte polarization accompany, rather than directly drive, resistance during long-term BTKi therapy.
This dataset is designed to be used with an analysis project which can be found on github at blaserlab/cll_scrnaseq: Repository for single cell analysis of BTKi resistance. Instructions for installation and for reproducing the figures and tables from the manuscript can be found on that site.