Dependence of IL-7R-Mediated Signaling on Sphingosine Kinase Activity in Acute Lymphoblastic Leukemia, but Not Healthy Lymphoid Cells, Is an Exploitable Therapeutic Vulnerability
Authors: Fernandes Marta B , Melão Alice , Araújo Tatiana , Cachucho Ana , Adams David R , Oh Jeongah , Almeida Afonso R M , Torta Federico , Barreto Vasco , Pyne Susan , Hla Timothy , Pyne Nigel J , Barata Joao T 
Published: December 2023

Acute lymphoblastic leukemia (ALL) is an aggressive cancer affecting B or T cell precursors. Interleukin 7 (IL-7) is essential for normal lymphoid development but shown also to contribute to ALL development and resistance to glucocorticoids. IL7R (the gene that encodes for IL-7 receptor α) is a bona fide lymphoid oncogene that is mutated in around 10% T-ALL and 3% B-ALL patients. Mutational activation of IL7R or high levels of wild type IL7R can drive ALL development in vivo. Sphingosine kinases, of which there are two isoforms (SK1 and SK2), generate sphingosine-1-phosphate (S1P) from sphingosine, thus promoting cell survival. We previously identified SKs as potential targets for therapeutic intervention in ALL with IL7R gain-of-function mutations. However, how IL-7R-mediated signaling crosstalks with SKs, and whether there is a therapeutic window for the use of SK inhibitors in ALL without provoking excessive side effects, remains to be determined.

Our thorough immunophenotypic characterization of CD2Cre.SK1 fl/fl.SK2 -/- mice, which display SK complete ablation exclusively in the lymphoid compartment, revealed no major impact on lymphoid development. Since, on the contrary, IL7R-null mice display severe B- and T-cell deficiency, this indirectly indicates that SKs are not involved in IL-7R-mediated signaling during lymphoid development. Accordingly, we found that healthy thymocytes and B-cell precursors did not require SK activity for IL-7-mediated signaling, as measured by the levels of STAT5 phosphorylation.

In sharp contrast, we found compelling evidence that SKs are involved in IL-7R-mediated signaling and functional impact in the context of leukemia. First, SK deletion in the lymphoid compartment significantlydelayed the development of B-ALL in mice with IL7R mutation in lymphoid precursors (CD2Cre.Il7r cpt/wt mice). Second, SK deletion impaired both basal and IL-7-mediated JAK/STAT5 pathway activation in leukemia cells from the same mice. In agreement, CRISPR-Cas9 SK1/SK2 gene editing in the human IL-7R-responsive HPB-ALL cell line prevented IL-7-induced JAK/STAT5 pathway activation and leukemia cell viability. Finally, pharmacological inhibition of SKs blocked IL-7-triggered viability of human patient-derived xenograft T-ALL cells, without significantly impacting healthy thymocytes.

We next sought to understand the reasons underlying IL-7R-mediated signaling aberrant dependence on SK activity in leukemia cells. Besides direct intracellular roles, S1P is exported to the extracellular compartment and able to induce autocrine or paracrine signaling via S1P receptors expressed at the cell surface. We found that S1PR4 transcript levels were upregulated in diagnostic T-ALL patient samples. Inhibition of S1PR4 downregulated IL-7-mediated JAK/STAT5 pathway activation in leukemia cells but not in healthy thymocytes. In agreement, S1P stimulation partially mimicked the effects of IL-7 exclusively in T-ALL cells. In addition, our analyses demonstrated that SK1 and SK2 are overexpressed in B- and T-ALL diagnostic patient samples. Importantly, we further report that SK1 co-immunoprecipitated with IL-7Rα in ALL cells and that SK1 overexpression upregulates IL-7R-mediated signaling in HeLa cells transfected with the IL-7R signaling machinery. Our results indicate that overexpression of SKs and/or S1PR4 may justify the augmented reliance of IL-7R-mediated signaling on SK activity displayed by ALL cells.

Finally, we demonstrated the potential therapeutic impact of our findings. The SK pharmacological inhibitor compound 49 reversed IL-7-dependent pro-survival effects in human B- and T-ALL samples in vitro. We then conducted a phase 2-like preclinical trial with 7 distinct IL-7-responsive T-ALL patient samples xenografted into immunodeficient mice, which showed that compound 49 significantly reduced disease burden (p=0.0156, Wilcoxon matched pairs signed rank test), with highest effects in the samples that displayed higher IL-7 signaling responsiveness.

Overall, our studies demonstrate that SKs are key players in oncogenic, but not in physiological, IL-7/IL-7R-mediated signaling. We uncover the importance of the SK-IL7R signaling crosstalk in ALL and pinpoint the therapeutic potential of SK inhibitors for IL-7R-dependent ALL.