Analysis of gene co-expression networks reveals mechanisms underlying synergistic antifungal treatment in S. cerevisiae
Background: Fungal pathogens are difficult to treat. There are few effective antifungal drugs available, and resistance is emerging. Iron chelators are promising synergents due to the importance of iron availability during host infection, but the mechanistic role of antifungal-chelator combinations is poorly understood. The project analyses cellular pathways that are differentially expressed during the synergistic response to elucidate the mechanisms and targets of drug-chelator treatment.
Method: To measure the effect of synergistic treatment on the S. cerevisiae transcriptome, cells were treated with i) amphotericin B only; ii) a combination of amphotericin B + lactoferrin, an iron chelator; and iii & iv) corresponding matching controls. RNA-seq data were generated using Illumina HiSeq 2000 with biological triplicates multiplexed and randomized across two sequencing lanes. Differential expression analyses were performed using EdgeR, and the results were co-visualized with biological networks using Cytoscape.
Results: Amphotericin B alone resulted in the down-regulation of nine genes involved in ergosterol biosynthesis and the up-regulation of AFT1, a transcription factor involved in iron transport. Amphotericin B + lactoferrin co-treatment halted AFT1 up-regulation and down-regulated genes involved in iron transport. These genes were co-expressed with YAP5, a second transcription factor that co-ordinates the expression of genes that control the nuclear localization of AFT1 and also governs the expression of oxidative stress response genes.