The human vault RNA enhances tumorigenesis and chemoresistance through the lysosome in hepatocellular carcinoma

The small non-coding <i>VTRNA1-1</i> (vault RNA 1–1) is known to confer resistance to apoptosis in several malignant cell lines and to also modulate the macroautophagic/autophagic flux in hepatocytes, thus highlighting its pro-survival role. Here we describe a new function of <i>VTRNA1-1</i> in regulating <i>in vitro</i> and <i>in vivo</i> tumor cell proliferation, tumorigenesis and chemoresistance. Knockout (KO) of <i>VTRNA1-1</i> in human hepatocellular carcinoma cells reduced nuclear localization of TFEB (transcription factor EB), leading to a downregulation of the coordinated lysosomal expression and regulation (CLEAR) network genes and lysosomal compartment dysfunction. We demonstrate further that impaired lysosome function due to loss of <i>VTRNA1-1</i> potentiates the anticancer effect of conventional chemotherapeutic drugs. Finally, loss of <i>VTRNA1-1</i> reduced drug lysosomotropism allowing higher intracellular compound availability and thereby significantly reducing tumor cell proliferation <i>in vitro</i> and <i>in vivo</i>. These findings reveal a so far unknown role of <i>VTRNA1-1</i> in the intracellular catabolic compartment and describe its contribution to lysosome-mediated chemotherapy resistance. <b>Abbreviations:</b> ATP6V0D2: ATPase H+ transporting V0 subunit d2; BafA: bafilomycin A1; CLEAR: coordinated lysosomal expression and regulation; CQ: chloroquine; DMSO: dimethyl sulfoxide; GST-BHMT: glutathionine S-transferase N-terminal to betaine–homocysteine S-methyltransferase; HCC: hepatocellular carcinoma; LAMP1: lysosomal associated membrane protein 1; LLOMe: L-leucyl-L-leucine methyl ester; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MAPK: mitogen-activated protein kinase; MITF: melanocyte inducing transcription factor; MTT: 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide; ncRNA: non-coding RNA; RNP: ribonucleoprotein; SF: sorafenib; SQSTM1/p62: sequestosome 1; STS: staurosporine; tdRs: tRNA-derived RNAs; TFE3: transcription factor binding to IGHM enhancer 3; TFEB: transcription factor EB; vtRNA: vault RNA transcript.