January 28th, 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, Amiri et al. (2024) aim to uncover how phosphorylated (p)-eIF2α influences translational control of naive pluripotency. Hofman et al. (2023) conducted ribosome profiling on 32 medulloblastoma tissues and cell lines, uncovering extensive translation occurring in non-canonical open reading frames. Lastly, Wacholder et al. (2023) utilize updated ribosome profiling and mass spectrometry techniques to explore the barriers limiting the identification of non-canonical proteins in yeast.
Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells
Cell Reports, 2024
Amiri, M., Kiniry, S.J., Possemato, A.P., Mahmood, N., Basiri, T., Dufour, C.R., Tabatabaei, N., Deng, Q., Bellucci, M.A., Harwalkar, K., Stokes, M.P. et al.
The integrated stress response (ISR) is crucial for cell survival during stress conditions. When faced with various environmental signals, eIF2α undergoes phosphorylation, triggering significant alterations in mRNA translation. While the ISR’s role is well understood in early embryonic development, the eIF2-dependent translational landscape in pluripotent embryonic stem cells (ESCs) remains to be explored. To delve into this, the authors employed a multi-omics approach—using ribosome profiling, proteomics, and metabolomics—in both wild-type (eIF2α+/+) and a mutant form lacking phosphorylation capability (eIF2αA/A) in mouse embryonic stem cells (mESCs). The aim is to uncover how phosphorylated (p)-eIF2α influences translational control of naive pluripotency.
In this study, they observed a temporary rise in p-eIF2α levels within the naive epiblast layer of E4.5 embryos. Notably, the absence of eIF2α phosphorylation leads to a departure from naive pluripotency following the withdrawal of 2i (two inhibitors of MEK1/2 and GSK3α/β). They found that p-eIF2α governs the translation of mRNAs responsible for controlling various aspects of pluripotency, chromatin arrangement, and glutathione synthesis. Consequently, p-eIF2α emerges as a crucial regulator within the gene regulatory network governing naive pluripotency.
Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma
Molecular Cell, 2023
Hofman, D.A., Ruiz-Orera, J., Yannuzzi, I., Murugesan, R., Brown, A., Clauser, K.R., Condurat, A.L., van Dinter, J.T., Engels, S.A., Goodale, A. et al.
One of the defining features of high-risk childhood medulloblastoma is the disruption in RNA translation. Yet, it remains unclear whether this cancer affects the translation of potentially cancerous non-canonical open reading frames (ORFs). To investigate, the authors conducted ribosome profiling on 32 medulloblastoma tissues and cell lines, uncovering extensive translation occurring in these non-canonical ORFs. Subsequently, they devised a systematic approach involving multiple CRISPR-Cas9 screens to identify non-canonical ORFs and potential microproteins that play a role in supporting the survival of medulloblastoma cells.
They discovered that several long non-coding RNA ORFs and upstream ORFs possess distinct functions independent of the primary coding sequences. Specifically, a microprotein stemming from one of these ORFs, ASNSD1-uORF or ASDURF, showed increased expression, linked to MYC-family oncogenes, and facilitated the survival of medulloblastoma cells by interacting with the prefoldin-like chaperone complex. These findings highlight the critical role of non-canonical ORF translation in medulloblastoma and advocate for the inclusion of these ORFs in future investigations aiming to identify novel targets for cancer treatment.
Biological factors and statistical limitations prevent detection of most noncanonical proteins by mass spectrometry
Plos Biology, 2023
Wacholder, A. and Carvunis, A.R.
Ribosome profiling shows extensive translation occurring in short open reading frames (ORFs) beyond known protein-coding genes. However, shotgun mass spectrometry (MS) experiments usually capture a minor portion of the anticipated protein products from this unconventional translation. This scarcity in detection might suggest rapid degradation of most predicted non-canonical proteins, rendering them absent in cells. Another possibility is that technical constraints hinder their detection. To delve into this, the authors utilized updated ribosome profiling and MS techniques to explore the barriers limiting the identification of non-canonical proteins in yeast.
Their research reveals that the limited identification of non-canonical ORF products is primarily due to their small size and low translation rates, rather than indicating their instability or lack of biological significance. Specifically, proteins stemming from newly evolved genes, even those with well-defined biological functions, tend to be too brief and inadequately expressed for current shotgun MS techniques to detect effectively. Furthermore, this investigation highlights how misleading estimates of false discovery rates for noncanonical proteins can arise from decoy biases, potentially leading to erroneous identifications. However, upon addressing these challenges, they were able to uncover compelling evidence for the existence of four non-canonical proteins in MS data, supported by evolutionary and translation evidence. These findings underscore the capability of MS in confirming unannotated genes predicted through ribosome profiling, while also emphasizing its limitations in detecting numerous biologically relevant yet lowly expressed proteins.