TRIM21 modulates stability of pro-survival non-coding RNA vtRNA1–1 in human hepatocellular carcinoma cells
EunBin Kong, Norbert Polacek
Abstract
Recent studies expanded our knowledge of diverse pro-survival functions of short non-coding vault RNAs. One of the human vault RNA paralogs, vtRNA1-1, modulates several intracellular processes, including proliferation, apoptosis, autophagy, and drug resistance in various types of human cancer cells. However, protein interaction partners and mechanisms by which vtRNA1-1 levels are controlled within the cells remained elusive. Here, we describe a regulatory process for vtRNA1-1 stabilization mediated by the newly identified interacting proteins, TRIM21 and TRIM25, in human hepatocellular carcinoma (HCC) cells. Depleting TRIM21 or TRIM25 reduced the stability of vtRNA1-1 both in vivo and in vitro.
Introduction
Recent studies of non-coding RNAs (ncRNAs) have shed new light on the flow of genetic information, even as the central dogma of molecular biology is still widely accepted. Across all three domains of life, a plethora of ncRNAs, transcripts that are not translated into proteins, are expressed from genomes to perform a variety of crucial cellular functions. Over the past years, regulatory functions of diverse ncRNAs, including long ncRNA, miRNA, snoRNA, siRNA, piRNA, and tRNA-derived RNA (tDR), have been identified. These various ncRNA ribo-regulators have in common the ability to fine-tune gene expression at all levels and hence have been implicated in disease in case of misregulation [1,2].
Materials and method
Cell culture, transfection and treatments
The human hepatocellular carcinoma cell line Huh7 WT and VTRNA1-1 KO (provided by Matthias Hentze; EMBL, Heidelberg, Germany), SNU423 and HepG2 (provided by Deborah Stroka; UniBe, Bern, Switzerland) and the human cervical cancer cell line HeLa (ATCC-CCL-2) were cultured in DMEM/F-12 (Gibco, 21331046) supplemented with 10% FBS (Gibco, 10082147) and 1x Pen-Strep glutamine (Gibco, 10378016). For reverse transfection of siRNA, Lipofectamine RNAiMAX (Invitrogen, 13778075) was used according to the manufacturer`s recommendations. For plasmid transfection or in vitro-transcribed RNA transfection, Lipofectamine 3000 (Invitrogen, L3000015) was used according to the manufacturer`s recommendations. Sorafenib tosylate (MedChemExpress, HY-10201A) was used from 10 to 14 μM for 24 hours. MG132 (Selleckchem, S2619) was used at 2 μM for 6 hours.
Results
Vault RNA1-1 interacts with TRIM21 and TRIM25
The function of ncRNAs in cells is determined by their interactions with other nucleic acids or proteins. Numerous ncRNAs interact with unique binding partners to perform specific roles. Over the past decades, the importance of RNA-protein interactions in modulating various cellular processes has become increasingly clear. As a potent regulator of cell viability and tumorigenicity, vtRNA1-1 (Fig 1A) interact with several proteins, such as p62/SQSTM and SRSF2 [13,16].
Discussion
It is no longer surprising that short ncRNAs play significant roles in regulating a multitude of cellular processes. In the past few decades, research has identified a diverse array of regulatory ncRNAs and elucidated their functions. Discovered in the mid-1980s [3], the short non-coding vtRNA has since been verified to regulate a variety of intracellular functions, including proliferation, apoptosis, and autophagy [4,7,10–13,16]. Specifically, a comprehensive and in-depth understanding of vtRNA1-1, which has pro-survival characteristics in many cancer cell lines of different tissue origin, could pave the way to developing novel therapeutic strategies or diagnostic approaches.
Acknowledgments
We would like to thank Matthias Hentze for providing the vtRNA1-1 knock-out Huh7 cell line and Markus Stoffel for providing the TRIM21 overexpression construct. Our thanks are extended to Max Wolfensberger and Marc Landolfo for experimental support.
Citation: Kong E, Polacek N (2025) TRIM21 modulates stability of pro-survival non-coding RNA vtRNA1–1 in human hepatocellular carcinoma cells. PLoS Genet 21(3): e1011614. https://doi.org/10.1371/journal.pgen.1011614
Editor: Shuguo Sun,, Huazhong University of Science and Technology Tongji Medical College, CHINA
Received: September 4, 2024; Accepted: February 10, 2025; Published: March 17, 2025
Copyright: © 2025 Kong, Polacek. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the manuscript and its Supporting Information files.
Funding: We acknowledge financial support by NCCR ‘RNA & Disease’ funded by the Swiss National Science Foundation [205601 to N.P.], and National Research Foundation of Korea [2022R1A6A3A03073455 to EB.K.]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
