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 suggest that T cell exhaustion and monocyte functional polarization may have a crucial role in BTKi resistance. Overall design: Peripheral blood was collected from patients with CLL patients with and without BTK resistance mutations. Samples were collected at diagnosis, time of detection of the BTK C481S mutation and at relapse. For those without mutations, samples were collected 3 and 5 years after diagnosis. Single cell immune profiling was performed using the 10X Genomics 5' capture technology with BCR and TCR sequencing.