Abstract
During autophagy, the coordinated actions of autophagosomes and lysosomes result in the controlled removal of damaged intracellular organelles and superfluous substrates. The evolutionary conservation of this process and its requirement for maintaining cellular homeostasis emphasizes the need to better dissect the pathways governing its molecular regulation. In our previously performed high-content screen, we assessed the effect of 1530 RNA-binding proteins on autophagy. Among the top regulators, we identified the eukaryotic translation initiation factor 4A-3 (eIF4A3). Here we show that depletion of eIF4A3 leads to a potent increase in autophagosome and lysosome biogenesis and an enhanced autophagic flux. This is mediated by the key autophagy transcription factor, TFEB, which becomes dephosphorylated and translocates from the cytoplasm to the nucleus where it elicits an integrated transcriptional response. We further identified an exon-skipping event in the transcript encoding for the direct TFEB kinase, GSK3B, which leads to a reduction in GSK3B expression and activity. Through analysis of TCGA data, we found a significant upregulation of eIF4A3 expression across several cancer types and confirmed the potential relevance of this newly identified signaling axis in human tumors. Hence, our data suggest a previously unrecognized role for eIF4A3 as a gatekeeper of autophagy through the control of TFEB activation, revealing a new mechanism for autophagy regulation.
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Data availability
All datasets generated and analyzed in this study are deposited at the GitHub repository (https://github.com/ELELAB/eIF4A3_RNASEQ) or provided in the supplementary information files.
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Acknowledgements
We thank Vanda Turcanova for assistance with cloning and Jernej Ule for helpful advice regarding the splicing analysis. We thank Valentina Cianfanelli for providing the CMV-Sigma14-TFEB-GFP plasmid and Andrea Ballabio for providing the TFEB phospho Serine 138 antibody. In addition, thanks to Anders H. Lund for constructive feedback and fruitful discussions regarding this work.
Funding
The work for this study was supported from The Lundbeck Foundation (R272-2017-3872), The Novo Nordisk Foundation (NNF19OC0056107), The Danish Cancer Society (R209-A13011), The Danish Council for Independent Research (DFF-7016-00313), and The Danish National Research Foundation (project CARD, DNRF 125).
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LBF developed the study concept; DS, THK, MHA, ARL, and LBF performed experiments; LB, MT, EP, and THK analyzed the sequencing and TCGA data; LBF, EP, and JB provided supervision; LBF, DS, and THK wrote the manuscript; all authors read and approved the final manuscript.
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Sakellariou, D., Tiberti, M., Kleiber, T.H. et al. eIF4A3 regulates the TFEB-mediated transcriptional response via GSK3B to control autophagy. Cell Death Differ 28, 3344–3356 (2021). https://doi.org/10.1038/s41418-021-00822-y
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DOI: https://doi.org/10.1038/s41418-021-00822-y
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