An epigenetic approach to fatty acid metabolism in haematological malignancies

Abstract

The role of fatty acids to overcome stress and contribute to disease progression is becoming increasingly evident in haematological diseases. Further, epigenetic factors play an important role in the aetiology of myelodysplastic syndromes (MDS) and the transformation to secondary acute myeloid leukaemia (sAML). To investigate this in the MDS/sAML cell line, SKK-1, we employed a shRNA knockdown screen to target 912 epigenetic regulators. We then coupled this loss-of-function approach to a fatty acid metabolism-based assay with which we were able to cell-sort the SKK-1 cells based on the fatty acid uptake. Here I describe the methodology of this epigenetics-metabolism approach and our efforts to validate candidate hits from the screen that were predicted to be modulators of fatty acid uptake. Following testing using single gene knockdowns of the top genes from the screen, we were not able to identify epigenetic regulators that significantly alter fatty acid uptake. In parallel, we characterised metabolic and genetic parameters of triple-sorted low (TS LOW) and high (TS HIGH) fatty acid uptake sub- populations. However, during the course of the study, we discovered latent contamination by another myeloid cell line, U-937, in our SKK-1 parental cells and TS LOW and TS HIGH sub-populations. Therefore, we interpreted results from the characterisation study with the knowledge that we had mixed cellular populations. I describe the steps we took to first identify the cell line and then our further characterisation of single cell clones of TS LOW and TS HIGH. Interestingly, we observed distinct cytogenetic profiles between single clones of TS LOW and TS HIGH, namely trisomy 8, which is a highly relevant chromosomal aberration in myeloid malignancies. Overall, this study provides a novel approach to investigate epigenetic and metabolic interactions in blood malignancies. We also find metabolically distinct sub-populations that differ by a disease-relevant karyotype.