Characterization of lncRNAs involved in lysosomal-associated death

Although the effects of inhibiting lysosome on post-transcriptional signaling pathways, such as autophagy, is being extensively study, the information on transcriptional alterations deriving by a blockade of lysosomal function is still incomplete, especially the one involving long non-coding RNAs (lcnRNAs). Attempting the identification of the transcriptional changes mediated by a lysosomal inhibition developed in our laboratory, 16200, we identified several lncRNAs which expression is significantly modulated by the treatment with our compound in melanoma A375 cells. Among them, PDK1-AS1 resulted in the long non-coding transcript mostly affected by 16200. Further analysis confirmed that PDK1-AS1 is activated upon the blockade of lysosomal function in diverse cancer cell lines and identified the preferentially expressed isoform and localization of this lncRNA. Combined genetic and pharmacological approaches revealed that PDK1-AS1 induction upon lysosomal inhibition depends on the activation of the master hypoxia regulator, HIF1α. Moreover, we provided data showing that 16200-mediated induction of HIF1α transcriptional response is partially mediated by the activation of the metabolic transcription factor, SREBP2, which derived from an impairment of cholesterol homeostasis. Of note, our transcriptomic analysis also identified additional 16200- activated lncRNAs, which expression have been reported to depend on hypoxia. Overall, our cellular and pharmacological assets provide a useful experimental system to investigate the molecular links between lysosomal function, metabolism and HIF1α signaling, as well as to explore the therapeutic opportunity of multitarget approaches modulating these pathways for treating cancer.