Metabolic Profiling Reveals Cellular Reprogramming of Acute Myeloid Leukemia By Omipalisib through Serine Synthesis Pathway

Background: More than 50% of AML patients had hyperactivation of PI3K-AKT-mTOR signaling. Those patients are supposed to be associated with poor prognosis and chemotherapy resistance. The PI3K-AKT-mTOR signaling involves many cellular processes, including mRNA translation, cellular metabolism, and protein turnover. Omipalisib is a dual PI3K/mTOR inhibitor that exhibits anti-tumor activity in several cancers. However, the precise metabolic consequences in response to PI3K/mTOR dual inhibitor are still not fully studied in AML.

Aims: To evaluate the efficacy and to elucidate the metabolic alteration of the anti-cancer effects of omipalisib on leukemic cells from both in vitro and in vivo aspects.

Materials and Methods: HL60, THP1, and OCI-AML3 myeloid leukemia cell lines were used in this study. Omipalisib (GSK2126458) was used for in vitro and in vivo experiments. Cell proliferation was measured by Cell Titer 96 AQueous One Solution Cell Proliferation Assay. The protein expression and phosphorylation status were analyzed by immunoblotting. Flow cytometry was used for cell cycle and mitochondrial analysis. The metabolomics profiles were analyzed by Agilent 1290 UHPLC system coupled with 6540-QTOF. RNA-seq was performed using an Illumina NovaSeq 6000 platform. Differentially expressed genes (DEGs) between control and omipalisib groups were identified by EBseq. A threshold of fold change ≥2 (or ≤0.5) and p ≤ 0.05 was used to select the DEGs. The mRNA quantification was measured by QuantStudio 3 Real-Time PCR Systems. The oxygen consumption rate (OCR) was analyzed by the XFe 24 extracellular flux analyzer. The CAnN.Cg-Foxn1 ^nu/CrlNarl mice were used for evaluating in vivo efficacy of omipalisib in murine model.

Results: We demonstrated the anti-proliferation effect of omipalisib on AML cell lines with different genetic background. The IC ₅₀ of OCI-AML3, THP1, and HL60 were 16.97nM, 9.35 nM, and 18.69 nM, respectively. Omipalisib could significantly induce G ₀/G ₁ cell cycle arrest in all three cell lines. As expected, omipalisib could significantly down-regulate the phosphorylation of AKT, mTOR, S6K and 4E-BP1. Metabolomics profiling analysis revealed that 24 of the 137 tested metabolites were significantly different between the control group and the omipalisib-treated groups in OCI-AML3 cells. Further metabolic pathway enrichment analysis demonstrated that metabolites related to amino acid metabolisms were significantly reduced following omipalisib treatment. In addition, we identified 300 DEGs between control and omipalisib-treated OCI-AML3 cells; of these, 251 were upregulated and 49 were downregulated. Further gene set enrichment analysis (GSEA) of hallmark gene sets indicated omipalisib treatment was significantly negatively associated with E2F targets, Myc targets, G2M checkpoint, mTORC1 signaling pathway, and oxidative phosphorylation. Joint-Pathway analysis (MetaboAnalyst 5.0) revealed that 'glycine, serine and threonine metabolism' was the most downregulated pathway in the omipalisib-treated group with p-value of 1.0076E-5 and impact value of 0.86567. qRT-PCR confirmed that several important genes, PHGDH, PSAT1, PSPH, SHMT1/2 and MTHFD1/2 in the serine and glycine synthesis pathway were significantly decrease in the OCI-AML3 cells following treated with omipalisib. OCR analysis indicated that the capacity of the mitochondria to produce energy was reduced after omipalisib treatment. Mitochondrial analysis showed that mitochondria mass and membrane potential decreased after omipalisib treatment, indicating the biosynthesis and functions of mitochondrial may be affected by omipalisib. In vivo studies showed that oral administration of 0.2 or 1 mg/kg omipalisib in mice could significantly retard tumor growth without obvious changes in body weight.

Summary: We found that nanomolar levels of omipalisib could significantly inhibit cell growth and induce G ₀/G ₁ cell cycle arrest in myeloid leukemia cells. Joint-Pathway analysis of RNA-seq and metabolomics data revealed that omipalisib mainly altered serine and glycine metabolism. Further experiments indicated that serine synthesis pathway could be suppressed by omipalisib at least in part through disrupting PI3K-AKT-mTOR signaling. In vivo xenograft model, omipalisib could retard tumor growth at as low as 0.2 mg/kg. This information may be potentially suitable for future clinical application.

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