The effects of AMPK activator A-769662 on the transcriptome of pathological phenotypes following mitochondrial DNA depletion

AMP-activated protein kinase (AMPK) is a master regulator of cellular energy homeostasis that also plays a role in preserving mitochondrial function and integrity. Upon a disturbance in the cellular energy state that increases AMP levels, AMPK activity promotes a switch from anabolic to catabolic metabolism to restore energy homeostasis. However, it is currently unclear how severe of a mitochondrial dysfunction is required to trigger AMPK activation, and whether stimulation of AMPK using specific agonists can improve the cellular phenotype following mitochondrial dysfunction. Using a cell model of mitochondrial disease characterized by progressive mitochondrial DNA (mtDNA) depletion and deteriorating mitochondrial metabolism, we show that mitochondria-associated AMPK becomes activated early in the course of the advancing mitochondrial dysfunction, before any quantifiable decrease in the ATP/(AMP+ADP) ratio or respiratory chain activity. Moreover, stimulation of AMPK activity using the specific small-molecule agonist A-769662 alleviated the mitochondrial phenotypes caused by the mtDNA depletion and restored normal mitochondrial membrane potential. Notably, the agonist treatment was able to partially restore mtDNA levels in cells with severe mtDNA depletion, while it had no impact on mtDNA levels of control cells. The beneficial impact of the agonist was also observed in cells from patients suffering from mtDNA depletion. However, the positive effects of A-769662 in the two experimental cell models appeared to involve at least partially different mechanisms. These findings improve our understanding of the effects of specific small-molecule activators of AMPK on mitochondrial and cellular function, and suggest a potential utility for these compounds in disease states involving mtDNA depletion. Uninduced and 4-day induced PolɣD1135A cells untreated or treated with 100 μM A-769662 for 72 h were grown to 80-90% confluence in 6-well plates, harvested and flash-frozen. Total RNA was extracted from cell pellets using Qiagen RNeasy Plus kit (QIAGEN) according to manufacturer’s instructions. Initial sample quality control was performed using Qubit and agarose gel electrophoresis. RNA libraries were prepared by Azenta Life Sciences using Illumina’s PolyA selection method, followed by sequencing on the Illumina NovaSeq platform with a 2x150 bp configuration, achieving a sequencing depth of approximately 20-30 million paired end reads per sample. Data files were assessed using FastQC, and read alignment was performed using STAR2.5.2b. On the WSL2 platform, featureCounts for Linux was utilized for quantification and generation of counts files.