Although mRNA decoding efficiency influences protein synthesis, it remains unknown whether the translation elongation machinery harbours intrinsic mechanisms that selectively modulate codon decoding to shape proteomes. Here we show that METTL13-catalysed dimethylation of the elongation factor eEF1A at lysine 55 (eEF1AK55me2) enhances decoding of select codons, preferentially increasing pro-oncogenic protein synthesis to promote tumorigenesis and targeted therapy resistance. Proteomic profiling and single-molecule imaging reveal that eEF1AK55me2 increases decoding efficiency, particularly for under-represented codons with weak wobble-position base pairing. In cancer cells, METTL13 knockdown reduced translation of oncogenic mRNA enriched in eEF1AK55me2-dependent codons, including KRAS; synonymous recoding with eEF1AK55me2-independent codons reversed this effect. METTL13 loss inhibited the growth of KRASG12C inhibitor (sotorasib)-resistant lung adenocarcinoma syngeneic tumours and patient-derived xenografts. In relapsed autochthonous KRASG12C-driven lung adenocarcinoma, METTL13 ablation mitigated sotorasib resistance and significantly extended survival in vivo. Among patients receiving a KRASG12C inhibitor, inferred METTL13 activity was associated with inferior clinical response. These findings identify an eEF1AK55me2-mediated mRNA decoding mechanism promoting selective oncogenic protein synthesis and suggest METTL13 targeting may counteract KRAS-inhibitor resistance.

Genome stability depends on the accurate repair of DNA double-strand breaks (DSBs). While chromatin-based mechanisms have been well studied, emerging evidence reveals that nuclear mechanics actively shape repair outcomes, although the mechanisms remain unclear. Here we identify microtubule acetylation as a regulator of nuclear mechanics that promotes DSB repair via homologous recombination (HR). DNA damage induces progressive tubulin acetylation, leading to displacement of the perinuclear vimentin cage. Loss of the vimentin cage softens the nucleus and renders the nuclear envelope responsive to microtubule forces, which drives transient nuclear shape fluctuations, localized DSB mobility and repair. Inhibiting tubulin acetylation abolishes these fluctuations, restricts DSB mobility and negatively impacts the homology search during HR, leaving non-homologous end joining intact. Consequently, persistent DSBs coalesce and cluster at the nuclear periphery, triggering cell-cycle arrest and senescence and increasing sensitivity to DNA-damaging agents. Removal of the vimentin cage is sufficient to rescue these effects, with restored nuclear fluctuations and repair efficiency. Thus, we propose that nuclear fluctuations act as a mechanical strategy to accelerate error-free repair. These findings reveal how cytoskeletal forces shape nuclear function and establish nuclear fluctuations as a fundamental principle for maintaining genome stability.

Migrating cancer cells release diverse extracellular vesicles (EVs) that carry cargo capable of influencing tumour progression and intercellular communication. However, the mechanisms by which intracellular components are incorporated into EVs remain poorly understood. Here we identify and characterize a previously undescribed population of large EVs (2-5 μm), termed motile vesicles (MoVes), that are generated during active cancer cell migration and associated with epithelial-mesenchymal transition. Comparative analyses across EV populations show that MoVes display distinct ultrastructural features, molecular composition and sedimentation behaviour. Live-cell imaging and scanning electron microscopy reveal that MoVes arise from trailing-edge retraction during mesenchymal migration and are actively shed by cancer cells but rarely by non-transformed cells. MoVes contain genomic DNA spanning the genome of the parent cell, recapitulating its mutational landscape, as well as organelles and proteins associated with epithelial-mesenchymal transition. Moreover, MoVes-associated mitochondrial cargo can enhance oxidative phosphorylation in recipient cells. Together, these findings identify MoVes as a cancer cell migration-associated EV population capable of disseminating genomic DNA and organelles.

Human embryo implantation begins with dynamic, tightly coordinated interactions between embryonic and endometrial compartments, yet the earliest trophoblast-endometrial interface dynamics remain poorly resolved in vivo. Here, using an endometrial assembloid-based three-dimensional co-culture system with human blastoids and natural blastocysts, we analyse implantation-like progression by time-series single-cell transcriptomics and functional perturbation. Importantly, we identify co-culture-induced trophoblast subsets marked by SDC1[+]MMP7[+] and enriched for transcriptional features associated with extracellular matrix remodelling and cell migration. These subsets are reproducibly detected across independent implantation-like systems, emerge specifically within a decidualized stromal co-culture context, and are further linked to stromal-derived CSF3 signalling by intercellular communication analysis and targeted perturbation. In parallel, the endometrium displays transcriptional changes associated with enhanced decidualization and a glandular hypersecretory transition. Together, our study provides a tractable framework for dissecting reciprocal embryo-endometrial adaptation at the onset of implantation.

The palmoplantar epidermis, in adapting to the exceptional mechanical strain it bears during locomotion, is histologically and molecularly distinct from other skin body sites. The mechanisms specifying and maintaining its unique identity remain incompletely defined. Here we identify the type I keratin 9 (KRT9/K9), a protein uniquely expressed in palmoplantar epidermis, as a key modulator of mechanosensitive YAP1 signalling in response to postnatal mechanical compression. K9 loss-of-function variants driving KRT9-pEDD, a palmoplantar epidermal differentiation disorder, result in aberrant YAP1 subcellular partitioning and elevated levels of the stress-induced keratin 16 (KRT16/K16). Krt9 null mice recapitulate these molecular phenotypes as early as postnatal day 3. We further identify dynamic, YAP1-dependent regulation of Krt16/K16, upstream of and necessary for Krt9/K9 expression, during early postnatal development in situ and in response to mechanical compression of keratinocytes ex vivo, highlighting the role of mechanical stress in epidermal specification. Mechanistically, K9 interacts with the YAP1 binding protein 14-3-3σ and sequesters YAP1 in the cytoplasm, inhibiting its transcriptional activity; these functions are disrupted by KRT9-pEDD-causing variants in K9. Finally, we show that genetic or pharmacological inhibition of YAP1 ameliorates palmoplantar keratoderma in Krt9 null mice. These findings reveal a role for mechanical cues in specification and maintenance of palmoplantar skin and suggest new therapeutic interventions for inherited palmoplantar epidermal differentiation disorders.

Ferroptosis is an iron-dependent type of cell death caused by excessive membrane lipid peroxidation. It remains a challenge to detect ferroptotic cells, especially in in vivo settings, hindering translational studies. Here we discover that a reducing reagent-resistant (3R) dimer of the transferrin receptor 1 (TfR1) is a highly specific indicator for lipid peroxidation. The 3R dimer is elevated in cells when ferroptosis is induced, either by pharmacological agents or by genetic perturbations. Furthermore, the 3R dimer can be used to detect disease-associated ferroptosis in tissue and in extracellular vesicles isolated from mouse or patient plasma. Given the near-ubiquitous expression of TfR1, we posit that the 3R dimer may function as a ferroptosis marker with widespread potential utility for basic and translational studies.

Organogenesis marks one of the most dynamic periods of early human embryonic development. Although the morphological features of this period have been described, the underlying transcriptional and metabolic landscapes remain poorly understood owing to the lack of an integrated spatial strategy. We present spatial transcriptomic and metabolomic maps of a Carnegie stage 12 (CS12) human embryo, co-registered with embryonic anatomy to generate a unified spatial multi-omic framework. Unsupervised clustering of the spatial transcriptomic data identified 17 cell populations covering the major organ primordia. Notably, we observed spatially separable hepatocyte- and cholangiocyte-lineage primed transcriptional programmes within the liver primordium, and detected cardiac outflow tract and sinoatrial node progenitors at CS12. Furthermore, integration of gene and metabolite abundance highlighted regional associations between transcription factors and metabolic pathways underpinning lineage specification. Our work presents a spatially resolved multi-omic atlas of a human embryo at the onset of organogenesis.

RNAs can associate with the surface of diverse cell types, yet the functions of specific RNA species on primary immune cells remain unclear. Here, utilizing methods developed to profile, image and quantify surface RNAs in rare primary cell populations, we found that Y RNAs, a family of small noncoding RNAs, preferentially localize to human monocyte surface. In an exploratory pooled inflammatory bowel disease cohort, the proportion of cell-surface-Y-RNA-positive peripheral monocytes was markedly higher in patients with inflammatory bowel disease than in healthy donors or individuals with irritable bowel syndrome. In vivo depletion of cell-surface Y RNAs ameliorates disease activity in mice with colitis. Mechanistically, cell-surface Y RNAs co-cluster with Toll-like receptors TLR2 and TLR4, bind extracellular histones and promote receptor-mediated histone recognition, thereby activating NF-κB and AP-1 signalling and increasing IL6 expression and IL-6 secretion. These findings identify cell-surface Y RNAs as previously unrecognized amplifiers of inflammatory activation.