Matched cerebrospinal fluid and bone marrow single cell transcriptomics highlights the CXCR4-CXCL12 axis in ALL CNS disease

Abstract Central nervous system (CNS) relapse in acute lymphoblastic leukemia (ALL) poses a significant clinical challenge. Although experimental studies have highlighted candidate genes for CNS involvement, studies in humans are scarce. We used single-cell transcriptomic profiling of leukemic cells in matched cerebrospinal fluid (CSF), bone marrow and blood of patients with ALL to identify genes and cell states associated with CNS involvement and relapse. CSF leukemic cells showed a distinct expression profile with lipogenic metabolic rewiring and occupied transcriptional states more closely related to bone marrow than to blood. Trajectory analysis identified six genes with progressively increased expression toward CSF-associated leukemic states (SMAP2, CXCR4, SPRY1, PLD1, HSPB1 and ARPP21). Among 16 genes previously implicated in ALL CNS disease in experimental models, CXCR4, SCD, VEGFA and SPP1 were significantly increased in CSF, and CXCR4 was further increased in patients with relapse (log2FC 2.1, p = 0.00096). Supporting this, patients with CNS relapse had higher soluble CXCL12 in CSF (p = 0.044) and higher bone marrow CXCR4 surface expression at diagnosis (p = 0.034) than patients without relapse. In conclusion, single-cell transcriptomics identified molecular alterations associated with ALL CNS disease. The CXCR4–CXCL12 axis stands out as a marker of CNS relapse in ALL and a promising therapeutic target.