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,

  • Rocha et al. find that SLC35A4-MP is a key regulator of mitochondrial lipid composition, structure, and oxidative function in brown adipose tissue.
  • Luo et al. describe a method of proximity-specific ribosome profiling.
  • Dian et al. find that DDX3X suppresses progression of KRAS-driven lung cancer.

Abnormal mitochondrial structure and function in brown adipose tissue of SLC35A4-MP knockout mice

Science Advances, 2025.

Rocha, A.L., Schmedt, C., Perkins, G., Pinto, A., Diedrich, J.K., Shan, H., Plucińska, K., Vieira de Souza, E., Vaughan, J.M., Foster, M., Sampath, S.C., Sampath, S.C., Cohen, P., Ellisman, M.H. and Saghatelian, A.

Sunday Paper 1

This study investigates the physiological role of SLC35A4-MP, a conserved 103–amino-acid microprotein encoded by an upstream open reading frame (uORF) in the Slc35a4 mRNA. Ribosome profiling and proteomics data were used to determine that while  the canonical SLC35A4 protein is not detectably translated in vivo, SLC35A4-MP is robustly expressed. It localizes to the inner mitochondrial membrane. The authors generated a SLC35A4-MP knockout (KO) mouse to examine its function, focusing on brown adipose tissue (BAT), a mitochondria-rich, thermogenic tissue where SLC35A4-MP is highly expressed.

SLC35A4-MP expression increases during brown adipocyte differentiation, high-fat diet (HFD) feeding, and cold exposure; conditions requiring elevated mitochondrial activity. Loss of SLC35A4-MP did not affect whole-body weight, glucose tolerance, or insulin sensitivity but caused pronounced BAT-specific defects. KO BAT exhibited smaller lipid droplets, reduced triacylglycerols, and broad alterations in mitochondrial lipids, including decreased cardiolipin and phosphatidylethanolamine and increased phosphatidic acid. Electron microscopy revealed enlarged, fewer, and more elongated mitochondria, indicating impaired mitochondrial dynamics.

Proteomics identified reduced mitochondrial metabolic proteins and increased inflammatory and extracellular matrix–remodelling markers. KO mice showed enhanced inflammation in BAT, with increased macrophage infiltration and cytokine expression. Functionally, KO brown adipocytes and macrophages displayed reduced oxidative respiration. During cold exposure, KO mice accumulated acylcarnitines, indicating defective fatty acid oxidation, and showed impaired acute thermogenic responses.

Overall, the study establishes SLC35A4-MP as a key regulator of mitochondrial lipid composition, structure, and oxidative function in BAT. Its absence disrupts metabolic resilience during stress, revealing microproteins as important contributors to thermogenic and mitochondrial biology.

Learn more about EIRNABio’s ribosome profiling services here.

Proximity-specific ribosome profiling reveals the logic of localized mitochondrial translation

Cell, 2025.

Luo, J., Khandwala, S., Hu, J., Lee, S.-Y., Hickey, K. L., Levine, Z. G., Harper, J. W., Ting, A. Y. & Weissman, J. S.

Sunday Paper 2

This study presents LOCL-TL, a light-activated, proximity-specific ribosome profiling method that maps translation at defined subcellular sites with codon-level resolution. LOCL-TL uses LOV-BirA, a blue-light–activated biotin ligase fused to an organelle-localized protein. Upon illumination, LOV-BirA biotinylates nearby Avi-tagged ribosomes, enabling selective purification and sequencing of ribosome footprints exclusively from the targeted compartment, providing high spatial specificity.

Applying LOCL-TL to the mitochondrial outer membrane (OMM), the authors identified which nuclear-encoded mitochondrial mRNAs are locally translated. These experiments were supported by standard ribo-seq, RNA-seq, mass spectrometry, and evolutionary analyses of mitochondrial proteins.

LOCL-TL revealed two distinct pathways governing localized mitochondrial translation. Long coding sequences initiate translation in the cytosol and are then recruited cotranslationally to mitochondria through a bipartite nascent-chain signal composed of a mitochondrial targeting sequence plus a downstream region that engages the import machinery. These long-CDS proteins are enriched for ancient metabolic enzymes of prokaryotic origin. In contrast, short coding sequences, including many electron transport chain subunits and mitochondrial ribosomal proteins, are targeted to the OMM before translation. This pathway depends on mRNA features such as introns and native UTRs rather than peptide signals. The RNA-binding protein AKAP1 mediates this pre-translational recruitment by binding short-CDS mRNAs, and AKAP1 loss selectively reduces their mitochondrial translation.

Overall, the study showcases LOCL-TL as a powerful, spatially resolved ribosome profiling strategy that reveals how different classes of mitochondrial proteins are targeted for localized translation, uncovering new principles of mitochondrial gene expression organization.

Learn more about EIRNABio’s ribosome profiling services here.

Targeting DDX3X suppresses progression of KRAS-driven lung cancer by disrupting antioxidative homeostasis and inducing ferroptosis

Cell Death & Disease, 2025.

Dian, M., Yun, L., Meng, Q., Lin, S., Ji, M., Zhou, Y., Liu, W., Yang, Z., Zhao, Y., Li, G., Jiang, J., Hao, W., Chen, Z., Zhou, Z., Zhang, R., Liu, T., He, Y., Yan, T., Wang, H., Cronin, S. J. F., Penninger, J.M., Cai, K., & Rao, S.

Sunday Paper 3

This study investigates the role of the RNA helicase DDX3X in KRAS-driven lung cancer and shows that inhibiting DDX3X suppresses tumour growth by disrupting antioxidant metabolism and inducing ferroptosis. DDX3X is elevated in KRAS-mutant tumours and supports redox balance by maintaining expression of key antioxidant enzymes. Using DDX3X knockout, shRNA/siRNA knockdown, and small-molecule degraders, the authors demonstrate that loss of DDX3X reduces proliferation across multiple KRAS-driven lung cancer models.

RNA-seq analysis of DDX3X-deficient cells revealed 768 downregulated and 1050 upregulated genes, with METTL16 emerging as a major transcriptionally suppressed target. METTL16 downregulation correlated with globally reduced m6A levels and was unique among m6A regulators. Integrating RNA-seq and proteomics highlighted a DDX3X–JUND–METTL16 regulatory axis required for maintaining cysteine and glutathione metabolism.

Polysome profiling showed that while CBS (cystathionine β-synthase, a key enzyme in cysteine synthesis) transcription and mRNA stability were unchanged, CBS translation was markedly reduced in DDX3X-deficient cells due to loss of METTL16-dependent m6A modification. In contrast, METTL16 itself showed no change in translational efficiency, confirming transcriptional control.

Functionally, DDX3X inhibition decreased glutathione synthesis, increased lipid peroxidation, elevated Fe²⁺, and sensitized cells to ferroptosis. Two DDX3X-targeting compounds, RK-33 and the PROTAC degrader J10, were tested, with J10 showing greater potency and reduced toxicity. In vivo, DDX3X loss significantly reduced tumour burden in KRAS-mutant mouse models.

Overall, the study identifies DDX3X as a central regulator of antioxidant homeostasis whose inhibition drives ferroptotic vulnerability, highlighting it as a promising therapeutic target in KRAS-driven lung cancer.

Learn more about EIRNABio’s ribosome profiling and polysome profiling services here.