Activation and exhaustion of CD8 T cells in patients with chronic lymphocytic leukemia treated with ibrutinib and pembrolizumab [scRNA-seq, scTCR-seq and bulk RNA-seq]

Single-agent anti-PD-1 antibodies lack clinical efficacy in patients with chronic lymphocytic leukemia (CLL). Here, we study the peripheral blood samples from high-risk or relapsed/refractory CLL before and after combination therapy of ibrutinib, fludarabine, and pembrolizumab (IFP). We performed bulk RNA-sequencing (bulk RNA-seq) to detect the transcriptomic changes of CLL and T cells during treatment, and demonstrated the immune responses of CD8 T cells to pembrolizumab by single-cell RNA sequencing (scRNA-Seq). Overall design: Multiomics scRNA-seq libraries (GEX, ADT, TCR) libraries were prepared using 10X Genomics platform using CD8+ T cells harvested from peripheral blood with negative selection using Miltenyi beads. Libraries from C1D1, C2D1 (after 1 cycle of pembrolizumab), and C9D1 (after 6 months of pembrolizumab) were marked with HTO hashtags and multiplexed prior to sequencing.