Identification of novel acid stress resistance genes and their roles in cancer cell growth

Abstract

A hallmark of all primary and metastatic tumours is their high rates of glucose uptake and glycolysis. A consequence of the glycolytic phenotype is the accumulation of metabolic acid, hence, tumour cells experience considerable intracellular acid stress. To compensate, tumour cells upregulate acid pumps, which expel the metabolic acid into the surrounding tumour environment, resulting in alkalization of intracellular pH and acidification of the tumour microenvironment. Nevertheless, we have only a limited understanding of the consequences of altered intracellular pH on cell physiology, or of the genes/pathways that respond to metabolic acid stress. We have used yeast as a genetic model for metabolic acid stress with the rationale that the metabolic changes that occur in cancer that lead to intracellular acid stress are likely fundamental. Using a quantitative systems biology approach we identified 129 genes required for optimal growth under conditions of metabolic acid stress. We identified six highly conserved protein complexes with functions related to oxidative phosphorylation (mitochondrial respiratory chain complex III and IV), mitochondrial tRNA biosynthesis (glutamyl-tRNA(Gln) amidotransferase complex), histone methylation (Set1C/COMPASS), lysosome biogenesis (AP-3 adapter complex) and mRNA processing/P-body formation (PAN complex). We tested roles for two of these, AP-3 adapter complex and PAN deadenylase complex, in resistance to acid stress using a myeloid leukemia-derived human cell line that we determined to be acid stress resistant. Loss of either complex inhibited growth of Hap1 cells at neutral pH and caused sensitivity to acid stress, indicating that AP-3 and PAN complexes are promising new targets in the treatment of cancer. That mutations in respiratory chain complexes are present in tumours having the glycolytic phenotype also suggests tumours are genetically sensitized to acid stress and will be susceptible to acid stress-directed therapies.