Functional SCD1 Is Critical for Acute Lymphoblastic Leukaemia Maintenance in the Central Nervous System

Abstract

The largest advance in survival rates for childhood acute lymphoblastic leukaemia (ALL) came with the recognition that eradication of disease in the central nervous system (CNS) is needed to achieve long-term cure. All modern ALL protocols include large amounts of CNS-directed therapy, predominantly with methotrexate, which can result in significant acute and chronic neurotoxicity. In addition, CNS relapse remains a clinical challenge with a lack of effective drugs for recurrent disease. Despite this, little is known about the mechanisms by which leukaemic blasts enter the CNS and survive in this different microenvironment. Identifying specific mechanisms that support maintenance of ALL in the CNS should facilitate more effective targeted therapies.CNS ALL blasts reside in the leptomeninges, bathed in cerebrospinal fluid (CSF) which is low in glucose, protein, lipids and oxygen. Since blasts need building blocks and energy to survive and proliferate, and CSF nutrient supplies are scarce, we hypothesized that changes in their metabolism would occur. Such metabolic remodelling (flexible adaptation of metabolism according to tissue location and environmental conditions) is acknowledged as a hallmark of cancers. In a nutrient-deprived environment such as the CSF, metabolic adaptations are likely to be key to ALL survival.Thus, we investigated specific CNS-related metabolic signatures of ALL blasts. NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice were xenotransplanted with two human ALL cell lines: SEM (t(4;11), MLL-AF4) and REH (t(12;21), ETV6-RUNX1). After engraftment, cells were isolated from the CNS and spleen and RNA sequencing performed (Next Seq500). Transcript quantification was done against both human and mouse transcriptomes, in order to remove any possible mouse RNA contamination. Stearoyl-CoA Desaturase (SCD1) and Fatty Acid Synthase (FASN), key enzymes involved in fatty acid synthesis, were among the most upregulated genes in the CNS. Single sample gene set enrichment analysis confirmed that fatty acid and lipid synthesis showed a clear and significant upregulation in blasts from the CNS compared to the spleen for both cell lines, whereas the opposite result was observed for fatty acid and lipid oxidation. These results were replicated using a publicly available human dataset comparing bone marrow (BM) vs. CNS relapse samples from ALL patients (GEO dataset GSE60926).We went on to characterise the fatty acid profile of normal CSF and paired plasma from both non-leukaemic NSG mice and healthy human volunteers. Both murine and human CSF are about 1000-fold less rich in fatty acids than plasma. Immunostaining of SCD1 and FASN confirmed that both enzymes were strongly expressed on ALL blasts in the leptomeninges of post-mortem samples from patients with CNS-relapse and xenograft models. Murine BM showed equivalent levels of FASN expression but lower SCD1, and western blots confirmed that SCD1 was overexpressed at the protein level by about 2-fold in CNS compared to spleen or BM. We therefore chose to pursue SCD1 as a potential therapeutic target for CNS leukaemia.Two groups of NSG mice were xenografted with SEM cells and treated from day 15 post-transplant with either vehicle or 5mg/kg of the oral small-molecule SCD1 inhibitor MF-438 daily for 11 days. This dose strongly impaired SCD1 activity, since the ratios of oleate to stearate in plasma from vehicle- treated mice were 6 times higher than in plasma from MF-438 treated mice. We confirmed that the drug also reduced intra-cellular ratios of oleate:stearate by approximately 2-fold. Measurement of ALL burden in the leptomeninges showed an approximately 50% reduction in the area of leukaemic infiltrates in brain-skull sections. No difference in the burden of leukaemia in BM could be identified, supporting a specific vulnerability to SCD1 inhibition in the CNS microenvironment.In conclusion, we report a strong fatty acid and lipid signature in ALL blasts retrieved from the CNS environment, and identify the enzyme SCD1 as a critical target. We show a significant upregulation of the enzyme, from RNA levels to enzymatic activity, both in murine and human samples of CNS ALL. Using a small-molecule inhibitor in vivo, we show that inhibiting SCD1 activity reduces the amount of CNS leukaemia. Altogether, our data identify fatty acid metabolism as a novel therapeutic target for CNS leukaemia. DisclosuresHalsey:Jazz Pharmaceuticals: Consultancy, Other: Support to attend educational meetings.