Autophagy refers to the catabolic process in eukaryotic cells that delivers 
cytoplasmic material to lysosomes for degradation. This highly conserved process 
is involved in the clearance of long-lived proteins and damaged organelles. 
Consequently, autophagy is important in providing nutrients to maintain cellular 
function under starvation, maintaining cellular homeostasis, and promoting cell 
survival under certain conditions. Several pathways, including mTOR, have been 
shown to regulate autophagy. However, the impact of lysosomal function 
impairment on the autophagy process has not been fully explored. Basic 
lipophilic compounds can accumulate in lysosomes via pH partitioning leading to 
perturbation of lysosomal function. Our hypothesis is that these types of 
compounds can disturb the autophagy process. Eleven drugs previously shown to 
accumulate in lysosomes were selected and evaluated for their effects on 
cytotoxicity and autophagy using ATP depletion and LC3 assessment, respectively. 
All eleven drugs induced increased staining of endogenous LC3 and exogenous 
GFP-LC3, even at non toxic dose levels. In addition, an increase in the 
abundance of SQSTM1/p62 by all tested compounds denotes that the increase in LC3 
is due to autophagy perturbation rather than enhancement. Furthermore, the gene 
expression profile resulting from in vitro treatment with these drugs revealed 
the suppression of plentiful long-lived proteins, including structural 
cytoskeletal and associated proteins, and extracellular matrix proteins. This 
finding indicates a retardation of protein turnover which further supports the 
notion of autophagy inhibition. Interestingly, upregulation of genes containing 
antioxidant response elements, e.g. glutathione S transferase and NAD(P)H 
dehydrogenase quinone 1 was observed, suggesting activation of Nrf2 
transcription factor. These gene expression changes could be related to an 
increase in SQSTM1/p62 resulting from autophagy deficiency. In summary, our data 
indicate that lysosomal accumulation due to the basic lipophilic nature of 
xenobiotics could be a general mechanism contributing to the perturbation of the 
autophagy process.