Memory-like natural killer cell and CD19-antibody based immunotherapy in combination with tyrosine-kinase inhibition of Ph(-like) acute lymphoblastic leukemia (RNA-Seq)

Epigenetic reprogramming determines transcriptional output of preactivated NK cells. We conducted RNA-sequencing on individually sorted NKC cells to analyze the transcriptional pattern of preactivated and canonical NK cells when exposed to K562 target cells.Gene set enrichment analysis (GSEA) of DEG analysis results showed a positive enrichment of the following Gene Ontology (GO) terms among others: Ribosome and mitochondrial function, immune system process, cell adhesion and motility. In general, the pre-activation of bead-isolated NK cells induced by IL12/15/18 and mbIL-21/4-1BB K562 expansion results in significant epigenetic reprogramming and enhanced transcriptional output. The epigenetic and transcriptional characteristics of IL12/15/18 pre-activated bead-isolated NK cells closely resemble those of mbIL-21/4-1BB K562 cell co-culture expanded NK cells, suggesting that a memory-like state can be induced in NK cells solely through IL21 4-1BB K562 co-culture conditions. We performed RNA-sequencing of single cell FACS-sorted NKC to determine the transcriptional activities of preactivated vs none preactivated NK cells upon K562 target cell exposure in a co-culture system. RNA sequencing was performed with a SMART-Seq mRNA kit from Takara for cDNA synthesis, and the library preparation was carried out using the Nextera XT kit from Illumina. The quality-controlled libraries were then sequenced on an Illumina NextSeq2000 in paired-end mode.