SLC5A3 Transports Myo-Inositol to Support the Growth of Acute Myeloid Leukemia

Metabolic reprogramming contributes to tumor development and sustains cancer cell proliferation. Like other cancers, acute myeloid leukemia (AML), a devastating hematologic malignancy with poor overall survival, has altered metabolic features, providing new possibilities for AML treatment. Since the niche can reshape the metabolic properties of cancer cells, it is critical to validate AML metabolic vulnerabilities in a proper microenvironment. To this end, we optimized a protocol for CRISPR screening in orthotopic xenograft AML models, including patient-derived-xenograft (PDX) models tractable for CRISPR-editing, to enable the systematic evaluation of the physiological relevance of top AML dependencies. We performed in vivo screens in MV4-11 and U937 cell lines and a PDX model, which converged to reveal the sodium/myo-inositol cotransporter SLC5A3 as a top-ranked in vivo gene target.

We have validated the SLC5A3 dependency in additional AML cell line and PDX models; SLC5A3 deletion consistently induced apoptotic cell death in all AML models tested. We also observed cell-context dependent alterations of cell cycle and differentiation. In addition, using a PDX model with a doxycycline-inducible CRISPR system, we have confirmed that induction of SLC5A3 knockout post transplantation significantly represses AML progression and prolonged mouse survival. Next, we investigated whether the growth defect caused by SLC5A3 knockout results from the myo-inositol deficiency. Augmentation of myo-inositol concentration in the standard culture medium completely rescued the proliferation of SLC5A3-knockout cells. In accordance, depletion of myo-inositol from the culture medium largely impeded the growth of parental AML cells, causing similar phenotypes as SLC5A3-deletion, with cell-context dependent alterations of cell cycle and induction of apoptotic cell death. Together, these data reveal that myo-inositol is a critical metabolite for AML.

Since a subset of AML cell lines were not dependent on SLC5A3 based on a genome-scale CRISPR screen dataset (DepMap), we explored the potential biomarkers associated with SLC5A3 essentiality in AML. Intriguingly, the low expression of Inositol-3-phosphate synthase 1 (ISYNA1) predicted a strong SLC5A3 dependency in AML cell lines. In addition to importing myo-inositol from the extracellular fluid, cells can also synthesize myo-inositol de novo from glucose 6-phosphate, and ISYNA1 encodes the rate-limiting enzyme in this myo-inositol biosynthesis pathway. We confirmed low expression of ISYNA1 protein in AML cells sensitive to SLC5A3 deletion, and importantly, overexpression of ISYNA1 can completely relieve the SLC5A3 dependency. Moreover, knockout of ISYNA1 in an ISYNA1-high cell line M07e exacerbated the growth defect associated with SLC5A3 deletion. Altogether, these results strongly demonstrate that SLC5A3 becomes essential in AML cells with insufficient myo-inositol biosynthesis capacity to support AML proliferation.

Finally, we have investigated the clinical features associated with low ISYNA1 expression in genomic datasets of primary AML samples, including TCGA and Beat AML, to postulate the patient population that can benefit from a SLC5A3-directed therapy. Interestingly, low ISYNA1 expression is associated with FAB M4 and M5 AML subtypes. In accordance, a monocyte lineage gene signature is enriched in ISYNA1-low samples. In addition, AML samples with low ISYNA1 expression tend to have IDH2 or DNMT3 mutations. Collectively, our study demonstrated that SLC5A3 is a strong metabolic dependency in AML, and targeting SLC5A3 can provide a therapeutic opportunity for a subset of monocytic AML.