Intracellular pH differentially regulates transcription of metabolic and signaling pathways in normal epithelial cells

Abstract

Intracellular pH (pHi) dynamics regulate normal cell functions while dysregulated pHi dynamics have been linked to disease. However, the molecular mechanisms linking pHi dynamics and cell biology are poorly understood. Here, we found that just 24 hours of altered pHi can trigger global transcriptional changes in normal human breast epithelial cells, particularly in signaling and metabolic pathways. We identified 176 genes that were differentially expressed with altered pHi, including Notch1 signaling and glycolytic pathway members. We confirmed pH-dependent expression of lactate dehydrogenase and pyruvate dehydrogenase kinase at the protein level and showed this produced a shift toward glycolytic metabolism at high pHi. We also found pH-dependent Notch1 expression and protein abundance, leading to increased downstream Notch1 signaling at high pHi. This work suggests transient pHi dynamics transcriptionally regulate signaling and metabolic pathways, identifies molecular targets driving pH dependent biology, and suggests pathways by which dysregulated pHi may drive disease.