Lysosomal Stress and Mitochondrial Dysfunction Define the Cellular Response to Photoactivated 1,9-Dimethyl-Methylene Blue

Conversely, bafilomycin upregulated genes related to lipid metabolism, cholesterol biosynthesis, and inflammatory signaling, while suppressing developmental and cytoskeletal programs. Interestingly, transcriptomic comparisons revealed a striking overlap between DMMB and bafilomycin signatures (95% concordant DEGs), suggesting a common transcriptome regulation. Among the several biological processes affected by DMMB, mitochondrial-related processes were strongly enriched.

To determine whether the acute transcriptome changes caused by DMMB led to persistent functional effects, we stimulated cells with DMMB and assessed mitochondrial respiration after a recovery period. Photoactivated DMMB reduced basal respiration, ATP production, proton leak, and maximal respiration, indicating sustained mitochondrial dysfunction. These effects were not further altered by bafilomycin co-treatment but were markedly exacerbated by rapamycin.

Collectively, we show that photoactivated DMMB leads to an extensive transcriptome rewiring, closely resembling autophagy inhibition with a sustained mitochondrial dysfunction. Our findings provide a valuable resource to understand the interplay between DMMB-induced lysosomal stress, transcriptional regulation, and PDT.