Mixed-lineage leukemia cells undergo unique adaptations in the CNS niche

KMT2A-rearranged (KMT2A-r) infant leukaemia can present as a lymphoid, myeloid or mixed lineage leukaemia and frequently involves the central nervous system (CNS), yet the impact of this lineage diversity and plasticity on CNS involvement remains poorly understood. Using a fully murine model of KMT2A-AFF1+ mixed lineage infant leukaemia, we investigated how the CNS niche influences the phenotype and function of leukaemia propagating cells (LPC). Previously defined bone marrow (BM)-derived LPCs were transplanted and shown to engraft the CNS, although not equally; LK/CLP cells were consistently underrepresented in the niche. Transplants of CNS-derived LPCs, modelling relapse, demonstrated reduced systemic repopulation capacity, with many recipients exhibiting stable long-term engraftment without developing overt leukaemia, a phenomenon not observed in BM-derived transplants. Transcriptomic profiling of matched CNS- and BM-derived LPCs revealed enrichment of pathways involved in hypoxia, lipid and cholesterol homeostasis, and inflammatory signalling. Notably, LPC subsets that successfully adapted to the CNS niche upregulated lipid and fatty acid metabolic programmes. CNS-derived LPCs showed increased expression of genes involved in T cell immune modulation, suggesting a skew to a more immunosuppressive environment. These findings indicate that the CNS niche imposes lasting metabolic, functional, and immunological constraints on leukemic cells, impairing their ability to reestablish systemic disease. We show that the CNS niche imposes selective pressures and causes functional reprogramming of mixed lineage LPCs, affecting their systemic repopulation capacity and, we hypothesise, immune cell interactions. We further believe this study has relevance to primary mixed lineage infant leukaemia and, increasingly important, lineage-switched infant leukaemia.