January 21st, 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, we first take a look into the world of RNA modifications, as Li et al. investigate the role of NSUN2 on codon-dependant translation, while later in this theme, Zhao et al. investigate the unexplored role of queuosine glycosylation, identifying the novel genes responsible. Finally, Patel et al. delve into the role of eEF1A2 in breast cancer, uncovering new links between its expression and several angiogenic factors.
The m5C methyltransferase NSUN2 promotes codon‐dependent oncogenic translation by stabilising tRNA in anaplastic thyroid cancer
Clinical & Translational Medicine, 2023
Li, P., Wang, W., Zhou, R., Ding, Y. and Li, X.
While most cases of thyroid cancer, such as differentiated thyroid cancer (DTC), have a favourable prognosis, others, such as anaplastic thyroid cancer (ATC), are aggressive and resistant to treatment. In cancer, the process of translation is often significantly altered, driven by a need to supply the tumour’s rapid growth rate or induce metastasis. tRNAs play a major role in translation, and are the most heavily modified RNAs in the cell. One of the most common modifications is m5C, catalysed predominantly by NSUN2, and it has been linked to the process of proliferation and stress response. Here, the authors sought to investigate the role of m5C in cancer, specifically ATC.
They find that NSUN2 is significantly upregulated in ATC compared to normal tissue, as well as to other types of thyroid cancer. RNA bisulfite sequencing in ATC revealed an enrichment of this modification in the T-loop and variable loop of tRNAs. Ribosome profiling in NSUN2 knockdown cells revealed decreased translational efficiency in proto-oncogenic genes such as JUNB, TRAF2, BCL2, RAB31, as well as c-Myc. Finally, the authors demonstrate that m5C methylated tRNAs tend to be more resistant to degradation, possibly contributing to increased protein synthesis with NSUN2 overexpression.
Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth
Cell, 2023
Zhao, X., Ma, D., Ishiguro, K., Saito, H., Akichika, S., Matsuzawa, I., Mito, M., Irie, T., Ishibashi, K., Wakabayashi, K. and Sakaguchi, Y. et al
tRNAs are the mostly heavily modified type of RNA, particularly so in the anticodon loop. Queuosine (Q), found at position 34 in tRNAs, is known to play a role in maintaining translational accuracy and efficiency. However, in certain tRNAs, such as for tyrosine and aspartate, Q is further modified with galactose and mannose, yielding galQ and manQ respectively. However, while the mechanisms behind Q function are slowly being unravelled, these extra modifications still remain relatively unexplored. Here, the authors aim to investigate these additional modifications, and the impact they may have.
In order to identify the enzymes responsible for the above modifications (named QTGAL and QTMAN respectively), the authors conducted diethylaminoethyl (DEAE) chromatography utilising further purification with ammonium sulphate and heparin treatment for QTGAL, and heparin and Resource Q for QTMAN. This purification identified B3GNTL1 and GTDC1 as the enzymes respectively responsible for QTGAL and QTMAN activity. Glycosylation had some codon-specific effects, with galQ significantly slowing down decoding at UAC codons, whereas manQ slowed down decoding at GAU and GAC codons. Interestingly, knockout of QTRT1, QTRT2, QTGAL, and QTMAN all increased levels of stop codon readthrough. These knockouts also induced a proteotoxic response, possibly explaining the previous observation. In zebrafish with genetic mutants for these genes, a slightly smaller survival rate was noticed, although a significantly shorter body length was observed, indicating a role for these genes in embryonic development.
EEF1A2 promotes HIF1A mediated breast cancer angiogenesis in normoxia and participates in a positive feedback loop with HIF1A in hypoxia
British Journal of Cancer, 2023
Patel, S.A., Hassan, M.K., Naik, M., Mohapatra, N., Balan, P., Korrapati, P.S. and Dixit, M
Breast cancer is a significant cause of cancer-related deaths in women, with metastasis drastically reducing survival rates. High microvascular density is associated with such metastatic potential, as well as cancer aggressiveness. Angiogenesis, i.e. the formation of new blood vessels, plays a crucial role in tumour growth, and is frequently triggered by hypoxic conditions. eEF1A, particularly the eEF1A2 isoform, has also been implicated in cancer progression, and previous studies have suggested a link between angiogenesis and expression of this isoform. However, the precise mechanisms of this relationship remain unclear. Here, the authors aim to delve into this relationship.
They find that, while eEF1A2 overexpression increases several angiogenic and proliferation parameters, eEF1A1, with which it shares 96% homology, does not. Similarly, while overexpression of eEF1A2 led to increased expression of VEGF (a key angiogenesis mediator), eEF1A1 did not. Hypoxic conditions, as well as HIF1A overexpression, also increased eEF1A2 levels. Interestingly, HIF1A inhibitors prevented eEF1A2 increases under hypoxia, suggesting this was the key mediator. Later, a HIF1A interaction site was identified in the eEF1A2 promoter, indicating it increases its expression transcriptionally. Later experimentation suggested that eEF1A2 increases VEGF transcription, as well as its translation. Delving deeper, the investigators uncovered a positive feedback loop, with eEF1A2 also found to promote HIF1A transcription via ERK-Myc and mTOR.