Single-cell RNA-seq of human bone marrow cells by TAS-Seq

The TCF3::HLF fusion protein defines a subtype of incurable B cell acute lymphoblastic leukemia (B-ALL). Here, we identified self-reinforcing IL-1b networks in TCF3::HLF B-ALL cells using a newly-established mouse model that fully recapitulates human TCF3::HLF B-ALL, including osteolysis. We found significant upregulation of several inflammatory cytokines, including IL1B, IL6 and IFNG in the B-ALL mice. Deletion of IL1B or IL1R1 strongly inhibited the growth of the human TCF3::HLF B-ALL cells, reduced the expression of RANKL and ameliorated the destruction of bone in the transplanted mice. Genetic and epigenetic analyses identified a previously unknown regulatory region of the IL1B gene locus, where TCF3::HLF directly binds. Importantly, single cell RNA-seq profiling of TCF3::HLF B-ALL patients revealed a dramatic upregulation of IL1B at relapse compared to the time of diagnosis. These findings suggest a critical role of TCF3::HLF-IL-1b axis for the progression of TCF3::HLF B-ALL. Cryopreserved bone marrow samples were obtained from two TCF3::HLF-positive B-ALL patients at diagnosis and at relapse. Healthy donor bone marrow mononuclear cells (BM MNC) were used as controls.