Single-cell network pharmacology predicts total therapies targeting multiple developmental clones in B-cell acute lymphoblastic leukemia

Taking the advantage of the human bone marrow (BM) scRNA-seq in Human cell atlas census of immune cells study, we resolved B lineage into comprehensive human B-cell development stages and identified their landscape in B-ALL. L-asparaginase is the cornerstone of combination protocols in acute lymphoblastic leukemia (ALL). After profiled B cell acute lymphoblastic leukemia (B-ALL) patient drug sensitivities ex vivo and applied network-based systems pharmacology analyses to examine signal circuitry, we revealed that the B-cell differentiation are correlated with the L-asparaginase response in B-ALL. Further multiomics analysis confirmed that L-asparaginase resistant B-ALL had higher percentage of Pre-pro-B like cells and less Pro-B like cells. By targeting BCL2, the key hub genes in Pre-pro-B cell network, Venetoclax combined with L-asparaginase can produce better outcome as demonstrated by in vitro and in vivo evaluations. In conclusion, our results identified B-ALL heterogeneity in L-asparaginase-resistant signature and BCL2 signaling and B-cell maturation stage, consistent with L-asparaginase response, providing unique opportunities for total clonal therapy. To check how the composition of B-cell development stage-like cells in B-ALL patients may indicate the drug response, we performed scMultiome profiling of two L-asparaginase sensitive (Ph-like_CRLF2, Near haploid) and two L-asparaginase resistant (KMT2A, Ph+) B-ALL cases. To further verify that L-asparaginase selectively kill the sensitive B cell population, we treated two L-asparaginase responsive B-ALL PDXs with L-asparaginase or vehicle ex vivo, followed by scMultiome analysis. To further check how the composition of B-cell development stage-like cells change after venetoclax treatment, We treated an available PDX sample with L-asparaginase, venetoclax, or both, and then performed scRNA-seq analysis.