October 6th, 2024
Recent Publications Harnessing the Power of Translatomics
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers, Gong et al. and Liu et al. investigated the role of the ac4c modification on both eEF1A2 and eEF2 in nasopharyngeal and hepatocellular carcinoma respectively, while Lu et al. examined the function of the m⁶A modification in hypoxic environments.
Targeting N4-acetylcytidine suppresses hepatocellular carcinoma progression by repressing eEF2-mediated HMGB2 mRNA translation
Cancer Communications, 2024
Liu, H., Xu, L., Yue, S., Su, H., Chen, X., Liu, Q., Li, H., Liang, H., Chen, X., He, J., Ding, Z and Zhang, B.
Hepatocellular carcinoma (HCC) has one of the highest mortality rates among cancers in the Western world. Several studies have drawn links between HCC and the RNA modification N4-acetylcytidine (ac4C), “written” by the NAT10 protein. This modification was initially observed in tRNA and rRNA, but recent research has documented widespread ac4C mRNA modification as well. This modification is primarily found in the 5’ UTR and CDS regions of mRNA, thought to discourage initiation in the former and encourage elongation in the latter. However, the precise mechanisms underlying its influence over translation remain unelucidated. Here, the authors investigate these mechanisms, and its relevance towards HCC progression.
Initially, they confirm high levels of ac4C modification and NAT10 expression in HCC tissue compared to healthy controls. Knockdown of NAT10 also significantly attenuated HCC colony formation and tumour growth, as well as the number of ac4C peaks, analysed via acRIP-seq. NAT10-deficient cells also demonstrated reduced monosome and polysome assembly, indicating a general decrease in protein synthesis. Ribosome profiling revealed that HMGB2, a protein involved in transcription and chromatin remodelling, was one of the most strongly downregulated at a translational level. Interestingly, RNA affinity chromatography noted that the ac4C modification had several strong translation-related binding proteins, particularly so eEF2 and SRP68. Indeed, eEF2 knockdown significantly reduced HMGB2 expression. Furthermore, they identify Panobinostat (a histone deacetylase inhibitor) as a strong antagonist of NAT10 catalytic activity, significantly reducing cell proliferation and invasion.
HIF‐1α‐induced expression of the m⁶A reader YTHDF1 inhibits the ferroptosis of nucleus pulposus cells by promoting SLC7A11 translation
Aging Cell, 2024
Lu, X., Li, D., Lin, Z., Gao, T., Gong, Z., Zhang, Y., Wang, H., Xia, X., Lu, F., Song, J. and Xu, G.
The nucleus pulposus (NP) is the soft, gel-like core of the intervertebral disk, where age related intervertebral disk degeneration (IVDD) frequently starts. The NP exists in a particularly hypoxic, nutrient-poor environment, where HIF-1α supports cell metabolism, encouraging glycolysis. Recently, in a hepatocellular carcinoma study, it has been shown that HIF-1α induced the expression of YTHDF1, a protein which can identify and bind to the m⁶A modification on mRNA, regulating their expression. Other studies have demonstrated the m⁶A is significantly dysregulated in IVDD, as well as iron regulation. Here, the authors aim to set out a theoretical framework of their collective role in IVDD.
Utilising IVDD patient NP tissue, they found decreased expression of GPX4, a potent ferroptosis inhibitor, as opposed to controls. Overexpression of HIF-1α reversed such an observation. Furthermore, the impact of ferrostatin-1, a synthetic ferroptosis inhibitor, was significantly attenuated following HIF-1α knockout, increasing its validity. Turning to YTHDF1, luciferase and ChIP-qPCR analysis suggests that HIF-1α binds to the YTHDF1 promoter, increasing its expression at the level of transcription. Interestingly, YTHDF1 overexpression led to similar impacts as seen with HIF-1α overexpression, suggesting they may be part of the same pathway. Indeed, knockout of YTHDF1 abolished any of the changes seen with HIF-1α overexpression. They theorise that YTHDF1 acts upon ferroptosis via regulation of SLC7A11, a cysteine and glutamate antiporter known to regulate ferroptosis. Knockout of YTHDF1 resulted in decreased levels of translation of the SLC7A11 mRNA. Indeed, when SLC7A11 was knocked out, the impact of YTHDF1 was lessened.
Ac4C modification of lncRNA SIMALR promotes nasopharyngeal carcinoma progression through activating eEF1A2 to facilitate ITGB4/ITGA6 translation
Oncogene, 2024
Gong, S., Qiao, H., Wang, J.Y., Huang, S.Y., He, S.W., Zhao, Y., Tan, X.R., Ye, M.L., Li, J.Y., Liang, Y.L. and Huang, S.W.
lncRNAs are characterised as non-coding RNAs longer than 200 nucleotides, and are thought to act as signals, scaffolds, or guide molecules, influencing a range of higher processes, including translation. eEF1A, on the other hand, is an elongation factor crucial for proper translation of coding mRNAs and is responsible for the enzymatic delivery of aminoacylated tRNAs to the ribosome, where they contribute to the elongation of nascent protein chains. There are two isoforms of this gene, displaying tissue-specific expression, with eEF1A2 garnering more interest due to its association with metastatic processes in cancer. Here, the authors investigate the role of lncRNAs in nasopharyngeal cancer (NPC), drawing links between them and the translation elongation machinery.
Using control and NPC patient samples, they reveal increased levels of the lncRNA SIMALR in NPC, and link it to poor prognosis, largely through its enhancement of cell migration and proliferation. RNA pulldown and FISH assays reveal that eEF1A2 was one of the strongest binding targets of this lncRNA. Knockdown of SIMALR did indeed decrease general protein translation, with further experimentation revealing that SIMALR promotes eEF1A2 phosphorylation, thus augmenting its GTPase activity, promoting elongation. RIP-Seq identifies mRNAs associated with the focal adhesion pathway as being associated with eEF1A2, thus linking SIMALR to their expression. Finally, they also link the ac4c modification (catalysed by NAT10) to SIMALR stability, thus adding to regulatory links surrounding eEF1A2 and its impact on NPC migration and proliferation.