Metabolism of Acute Myeloid Leukemia Cell Lines Alters with Passage in 2D Culture and Remains Stable in 3D

Acute Myeloid Leukemia (AML) is a heterogeneous and complex malignancy of the blood and bone marrow (BM). Current treatment options only cure 40% of patients under the age of 65 years and, over the age of 65 years only 10% will be cured. Hence, there is great urgency to further understand pathogenesis, optimize treatment and identify markers for diagnosis, prognosis and targets for novel therapies.

It is increasingly evident that metabolism and BM microenvironment are key factors in AML pathogenesis and progression - entities that cannot be accurately investigated within current in vitro methods of two-dimensional (2D) culture. The metabolome is the final downstream product of gene transcription that also responds dynamically to its environment. Metabolomics is an established technique to identify biomarkers with prognostic relevance, such as 2-hydroxygluterate, an onco-metabolite derived from IDH mutations in AML. Targeting metabolic pathways such as oxidative phosphorylation, glycolysis and specific mutations that affect metabolism such as isocitrate dehydrogenase are currently being assessed in clinical trials. An in vitro system that could more accurately represent the in vivo BM may help optimise these metabolically-targeted regimens. Here we show that a previously established three-dimensional (3D) culture within our laboratory recapitulates elements of BM structure enabling long-term culture of AML cell lines without disrupting metabolism, as is the case with serial passage in 2D culture. Metabolism was assessed using gas chromatography-mass spectrometry (GC-MS) metabolomics analysis which reflects the phenotype of the leukemic cell lines.

Porous polyurethane scaffolds were fabricated using dioxin by thermally induced phase separation as previously described; scaffolds have a pore size of 100-250µm and a porosity of 90-95% cut to 0.5cm³, coated with type I collagen and seeded with 0.5x10⁶cells of either K562 (erythroleukemia) or HL-60 (promyelocytic leukemia) cells, after expansion in 2D culture. In parallel, 2D cultures of the same cell lines were maintained using passage every 2 days. K562 and HL-60 cells were cultured in IMDM, 1% penicillin and streptomycin and 20% or 10% foetal bovine serum, respectively. Serial sampling occurred at 4 time points over 21 days from 10 scaffolds of each condition. Cells were extracted from the 3D scaffolds using two techniques - needle extraction or TrypLE express (Thermo Fisher Scientific) to assess whether these physical or chemical extraction methods disrupt the metabolome. Once cells were extracted, they were suspended in methanol at 1x10⁶cells/mL cold methanol for metabolite quenching; metabolites were subsequently extracted with methanol/water and derivatised with Methoxamine and N-Methyl-N-(trimethylsilyl)trifluoroacetamide. Metabolomics analysis was then performed using a Shimadzu QP2010 Ultra GC-MS machine detecting 138 metabolites including those of pertinent pathways: glycolysis, tricarboxylic acid, pentose phosphate, urea, glutaminolysis and amino acids. Bioinformatics analysis was performed with MeV TM4(http://mev.tm4.org).

Using unsupervised clustering techniques, including hierarchical clustering and principal component analysis, we identified that the metabolome of TrypLE express and needle-extracted cells from 3D scaffolds have a similar metabolic signature and group closely with each other as well as with the metabolome of the seeded cells (day 0); they do not vary significantly over the 21 days of culture. Conversely, with each passage, the metabolomes of the 2D-cultured cells differ to those of day 0 and vary to each other over the same 21-day period.

These results highlight limitations in the use of 2D cultures to address AML biology as metabolic changes with passage reflect change in phenotype. Based on these findings, we conclude that 3D cultures provide a more stable environment for leukemic cell culture and assessment of leukemia biology, irrespective of method of cell extraction. The 3D culture platform is more suited than standard 2D in vitro cultures to investigate metabolism, microenvironment and drug targets in AML.