Impact of Acute or Chronic Acidosis and Hypoxia on Gene Expression Patterns in Tumour Cells: Potential Functional Implications.

Tumours often exhibit pronounced hypoxia and hereby extracellular acidosis due to intensified glycolysis. Since metabolic parameters can modulate gene expression, the aim of the study was to analyse changes in gene expression patterns induced by acute (24 h) acidosis or hypoxia and also in tumour cells adapted to long-term acidosis (5 weeks). Three tumour cell lines (AT1 prostate carcinoma, MCF-7, and MDA-MB-231 breast carcinoma) were exposed to acidosis (pH 6.6) or hypoxia (pO 1.5 mmHg) for 24 h. For long-term acidosis, AT1 tumour cells were continuously cultured at pH 6.6 for 5 weeks. Gene expression was examined by total RNA-sequencing and the functional significance was assessed by gene set enrichment analysis using the Gene Ontology database. Under short-term acidosis (24 h), AT1 and MCF-7 cells showed comparable changes. 714 genes were acidosis-dependently regulated in AT1 cells (275 up, 439 down), and 221 genes in MCF-7 cells (95 up, 126 down). MDA-MB-231 cells almost did not respond to low pH (13 regulated genes). Hypoxia affected MCF-7 cells the most (1498 regulated genes), whereas fewer genes were regulated in AT1 and MDA-MB-231 cells. Concerning the function of the regulated genes by short-term acidosis, RNA processing, cell cycle regulation, DNA synthesis, and mitochondrial function were negatively affected. Chronic acidosis showed a different picture. In AT1 cells, 1160 genes were differentially expressed (638 up, 522 down) when cells exposed to low pH for 5 weeks. The putatively acidosis-induced changes in functions included tissue structural development, RNA processing, and mitochondrial activity. This study shows that both acute and chronic acidosis of tumour cells lead to altered gene expression and thus affect cell function. Long-term acidosis leads to fundamentally different changes, indicating an adaptation process of the tumour cells.