Acid suspends the circadian clock in hypoxia through inhibition of mTOR

Recent reports indicate hypoxia influences the clock through the transcriptional activities of hypoxia inducible factors (HIFs) at clock genes. Unexpectedly, we uncover a profound disruption of the circadian clock and diurnal transcriptome when hypoxic cells are permitted to acidify, recapitulating the tumor microenvironment. Buffering against acidification or inhibiting lactic acid production fully rescues circadian oscillation. Acidification of several human and murine cell lines, as well as primary murine T cells, suppresses mechanistic target of rapamycin complex 1 (mTORc1) signaling, a key regulator of translation in response to metabolic status. We find acid drives peripheral redistribution of normally perinuclear lysosomes, inhibiting lysosome-bound mTOR. Restoring mTORc1 signaling and the translation it governs rescues clock oscillation, revealing a model in which lactic acid produced during the cellular metabolic response to hypoxia suppresses the circadian clock through diminished translation of clock constituents. RNA-sequencing was performed over a 52-hour timecourse using total RNA collected every 4 hours from U2OS human osteosarcoma cells in media of pH 7.4 or pH 6.3