RNA-seq analysis of an acute myeloid leukaemia cell line treated with phenolic compounds

Abstract

It is hard to overstate the revolutionary changes brought about by next-generation sequencing to the realm of biomedical research. RNA sequencing (RNA-seq) is an application of such methods used to quantify the gene expression of a biological sample at a given moment. Measurable variances in gene expression bring about differing cellular characteristics, including the hallmarks of cancer. An RNA-seq pipeline was developed to analyse gene expression data of the HL-60 Acute Myeloid Leukaemia (AML) cell line. Differential gene expression analysis was performed on three samples treated with phenolic compounds derived from extra virgin olive oil against a negative control to determine whether the treatment was successful in inducing differentiation. Each of the treated samples was taken at a different time interval after treatment (1 hr, 6 hr and 12 hr) so that the temporal aspect of differentiation may be observed. This study aims to determine whether the phenolic treatment was effective in inducing differentiation in HL-60 cells, and to determine the phenolics-induced effects on the transcriptome over time. We hypothesised that the treated cells would exhibit a significant down-regulation of genes associated with cell proliferation, and a significant up-regulation of genes associated with myeloid differentiation and apoptosis when compared to untreated cells. Over time we expect that the magnitude of the difference in expression, and the statistical significance of its presence will increase over time. Results show signs of myeloid differentiation across the treated samples, with a down-regulation of genes (p<0.001, adjusted for multiple testing) related to proliferative action (CCL2, FOSB), transmigration (JAML, FOSB, CEACAM6) and apoptotic inhibition (S100A4), all of which are characteristic of cancerous cells, while up-regulated genes have assorted metabolic functions (UTP14C, ALDH1L2, ADM2, SLC7A11, CBS). Principal component analysis of normalised gene counts suggest a distinctive transcriptomic composition of the 1 hr sample, contrasting with the similarities between the 6 hr and 12 hr samples