April 6th, 2025
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,
- Doglioni et al. find that eIF5A hypusination-driven translation promotes lung metastasis by enhancing collagen synthesis in cancer cells.
- Roiuk et al. find that eIF2A plays little to no role in regulating translation initiation in human HeLa cells.
- Hou et al. find that MAPKBP1 promotes apoptosis in response to radiation and its translation is regulated by uORF.
Aspartate signalling drives lung metastasis via alternative translation
Nature, 2025
Doglioni, G., Fernández-García, J., Igelmann, S. et al.
The lung often becomes an organ of metastasis across various cancers – 54% of patients with metastatic tumours have lung metastases. The mechanism explaining aggressiveness of lung metastases has not yet been elucidated. To investigate that, scientists used single-cell RNA-sequencing (scRNA-seq) and polysome-seq of metastasis growing in healthy lungs and in lungs primed with tumour-secreted factors (TSFs) taken from 4T1 breast tumours in mice. Scientists observed the increased translation of eIF5A in aggressive 4T1 and EMT6.5 lung metastases from TSF-treated mice in comparison to controls. This activation of eFI5A can be explained by hypusination – exclusive to eIF5A post-translational modification. Inhibiting the first enzymatic step of hypusination led to a decrease of the metastasis aggressiveness induced by TSFs suggesting that the aggressiveness of lung metastases is mediated by eIF5A hypusination.
Further investigation highlighted the role of aspartate whose increased levels were found in lung interstitial fluid of TSF-primed mice. Cancer cells pre-treated with aspartate led to an increased metastasis aggressiveness, while inhibiting eIF5A hypusination decreased the aspartate-induced metastasis aggressiveness. Polysome-seq revealed the translational program activated downstream of eIF5A, highlighting strong signatures of TGFβ signaling. In aspartate-treated tumors, COL1A1 expression and type I collagen abundance were notably increased. These findings suggest that eIF5A hypusination-driven translation promotes metastasis by enhancing collagen synthesis in cancer cells through TGFβ signaling. Similar discoveries were shown in patients with breast cancer.
Learn more about EIRNA Bio’s polysome profiling service here.
Human eIF2A has a minimal role in translation initiation and in uORF - mediated translational control
eLife, 2025
Roiuk M., Neff M., and Teleman A.A.
eIF2A has long been recognized as a translation initiation factor due to its ribosome binding and genetic interactions with other initiation factors, though its exact role has remained unclear. However, this study challenges that understanding. Roiuk et al. used ribosome profiling, polysome profiling, and reporter assays to systematically demonstrate that eIF2A does not function as a translational factor in HeLa cells. To investigate its role further, they generated eIF2A knock-out HeLa cells. eIF2A knockout (KO) cells showed no defects in proliferation rates, supporting the idea that eIF2A plays a largely dispensable role in organismal viability. Polysome profiling revealed no noticeable differences in polysome distribution between eIF2A KO and control cells. Additionally, ribosome profiling identified only 15 genes, apart from eIF2A itself, with altered translation efficiency between WT and KO cells, indicating that eIF2A has a minimal role in translation regulation. Furthermore, no significant changes were observed in near-cognate-initiated uORF translation.
Another proposed function of eIF2A is serving as a backup tRNA delivery mechanism under stress conditions when eIF2α is inactivated by phosphorylation. To investigate this, ribosome profiling was conducted in WT and eIF2A KO cells treated with tunicamycin to induce eIF2α phosphorylation. The results showed that, similar to non-stressed conditions, eIF2A had minimal impact on global translation even when eIF2α activity was reduced. No significant translational changes were observed in individual transcripts either. Overall, this study supports the idea that eIF2A plays little to no role in regulating translation initiation in human HeLa cells.
Learn more about EIRNA Bio’s ribosome profiling and polysome profiling services here.
Ribosome profiling reveals dynamic translational landscape in HEK293T cells following X-ray irradiation
Genomics, 2025
Hou J., Yu L., Wu C., Wei S., and Gao X.
X-ray exposure induces DNA damage and activates the DNA damage response (DDR), leading to widespread gene expression changes. However, a comprehensive understanding of mRNA translation following X-ray irradiation remains incomplete. To address this, researchers performed ribosome profiling and polysome profiling in HEK293T cells to investigate translational changes. Their findings revealed a significant inhibition of protein synthesis at 4 hours post-exposure, which recovered by 12 hours, highlighting the suppressive effect of X-ray radiation on translation. Polysome profiling further showed a marked decrease in polysome fractions and a corresponding increase in monosome fractions at the 4-hour mark. Integrating ribosome profiling with RNA sequencing, the study found that translational regulation played a more prominent role than transcriptional regulation under X-ray treatment.
Among the translationally upregulated genes, several contained potential upstream open reading frames (uORFs), including the previously reported DDIT3 and a novel regulator, MAPKBP1. Under normal conditions, MAPKBP1 translation is suppressed by uORF-mediated inhibition, but this repression is lifted following X-ray-induced stress, leading to increased CDS translation. Functional analysis demonstrated that MAPKBP1 knockdown reduced apoptosis and enhanced cell viability in HCT116 cells after X-ray exposure, suggesting its role in promoting apoptosis in response to radiation. Additionally, the study identified 601 actively translated small open reading frames (smORFs) within long non-coding RNAs (lncRNAs), with over 70% originating from processed transcripts. One smORF, found in lncRNA RP11-6N17.4, was confirmed to produce a stable peptide in HEK293T cells, the synthesis of which was abolished upon start codon mutation. This peptide may play a regulatory role in DDR, further expanding our understanding of the translational response to X-ray radiation.
Learn more about EIRNA Bio’s ribosome profiling and polysome profiling services here.