EMBO Reports最新文献

Hypoxia is both a physiological and pathological signal in cells. Changes in gene expression play a critical role in the cellular response to hypoxia, enabling cells to adapt to reduced oxygen availability. These changes are primarily mediated by the HIF family of transcription factors, however, other transcription factors such as NF-κB, are also activated by hypoxia. Although NF-κB is known to be activated by hypoxia, the extent to which NF-κB contributes to the hypoxic response remains poorly understood. Here, we analysed hypoxia-induced, NF-κB-dependent gene expression, to define the NF-κB-dependent hypoxic signature. Our analysis reveals that most genes downregulated by hypoxia require NF-κB for their repression. We show that although the NF-κB-mediated hypoxic response may vary between cell types, a core subset of hypoxia-inducible genes requires NF-κB across multiple cell backgrounds. We demonstrate that NF-κB is critical for reactive oxygen species (ROS) generation and regulation of genes involved in oxidative phosphorylation under hypoxia. This work highlights NF-κB's central role in the hypoxia response and offering new insights into gene expression regulation by hypoxia and NF-κB.

The brain's perineuronal extracellular matrix (ECM) is a crucial factor in maintaining the stability of mature brain circuitry. However, how activity-induced synaptic plasticity is achieved in the adult brain with a dense ECM is unclear. We hypothesized that neuronal activity induces cleavage of ECM, creating conditions for synaptic rearrangements. To test this hypothesis, we investigated neuronal activity-dependent proteolytic cleavage of brevican, a prototypical ECM proteoglycan, and the importance of this process for functional and structural synaptic plasticity in the rat hippocampus ex vivo. Our findings reveal that chemical long-term potentiation (cLTP) triggers rapid brevican cleavage in perisynaptic regions through the activation of an extracellular proteolytic cascade involving proprotein convertases and ADAMTS-4 and ADAMTS-5. This process requires NMDA receptor activation and involves astrocytes. Interfering with cLTP-induced brevican cleavage prevents the formation of new dendritic protrusions in CA1 but does not impact LTP induction by theta-burst stimulation of CA3-CA1 synapses. Our data reveal a mechanism of activity-dependent ECM remodeling and suggest that ECM degradation is essential for structural synaptic plasticity.

Argonautes are ancient proteins with well-characterised functions in cell-autonomous gene regulation and genome defence, but less clear roles in non-cell-autonomous processes. Extracellular Argonautes have been reported across plants, animals and protozoa, yet their biochemical and functional properties remain elusive. Here, we demonstrate that an extracellular Argonaute (exWAGO) released by the rodent-infective nematode Heligmosomoides bakeri is detectable inside mouse cells during the natural infection. We show that exWAGO is released from H. bakeri in both vesicular and non-vesicular forms that have different resistances to proteolysis, different accessibilities to antibodies and associate with different subsets of secondary siRNAs. Using recombinant exWAGO protein, we demonstrate that non-vesicular exWAGO is internalised by mouse cells in vitro and that immunisation of mice with exWAGO confers partial protection against subsequent H. bakeri infection and generates antibodies that block exWAGO uptake into cells. Finally, we show that properties of exWAGO are conserved across Clade V nematodes that infect humans and livestock. Together, this work expands the context in which Argonautes function and illuminates an RNA-binding protein as a vaccine target for parasitic nematodes.

Human immune protection against bacteria critically depends on activation of the complement system. The direct bacteriolytic activity of complement molecules against Gram-negative bacteria acts via the formation of Membrane Attack Complex (MAC) pores. Bactericidal MAC pores damage the bacterial outer membrane, leading to destabilization of the inner membrane. Although it is well-established that inner membrane damage is crucial for bacterial cell death, the critical event causing MAC-mediated inner membrane damage remains elusive. Here we question whether the bacterial cell envelope possesses vulnerable spots for MAC pores to insert. By following the localization of MAC pores on E. coli over time using fluorescence microscopy, we elucidate that MAC deposition initiates at the new bacterial pole, which induces inner membrane damage and halts bacterial division. MAC components C8 and C9 preferentially localize at new bacterial poles, while C3b localizes randomly on the bacterial surface. This suggests that preferential MAC localization is determined by one of the initial steps of MAC formation. These findings provide valuable information about the interplay between immune components and the Gram-negative cell envelope.

Mutations in KRAS, particularly at codon 12, are frequent in adenocarcinomas of the colon, lungs and pancreas, driving carcinogenesis by altering cell signalling and reprogramming metabolism. However, the specific mechanisms by which different KRAS G12 alleles initiate distinctive patterns of metabolic reprogramming are unclear. Using isogenic panels of colorectal cell lines harbouring the G12A, G12C, G12D and G12V heterozygous mutations and employing transcriptomics, metabolomics, and extensive biochemical validation, we characterise distinctive features of each allele. We demonstrate that cells harbouring the common G12D and G12V oncogenic mutations significantly alter glutamine metabolism and nitrogen recycling through FOXO1-mediated regulation compared to parental lines. Moreover, with a combination of small molecule inhibitors targeting glutamine and glutamate metabolism, we also identify a common vulnerability that eliminates mutant cells selectively. These results highlight a previously unreported mutant-specific effect of KRAS alleles on metabolism and signalling that could be potentially harnessed for cancer therapy.

TFE3 orchestrates cellular responses to a variety of stress conditions, promoting restoration of cellular homeostasis and cell survival. Here we report the presence of two different TFE3 isoforms generated by the use of alternative transcription initiation sites. The long isoform (TFE3-L) undergoes continuous proteolytic degradation due to the presence of a phosphodegron in its N-terminal region and only accumulates under specific stress conditions. In contrast, the short isoform (TFE3-S) lacks the first 105 residues containing the phosphodegron and is constitutively expressed at high levels in most cell types. Both isoforms share the same Rags/mTORC1-dependent mechanism of regulation and display comparable capacity of inducing expression of lysosomal and autophagic genes upon activation. However, TFE3-L is considerably more efficient than TFE3-S promoting cell migration and invasion. Accordingly, specific TFE3-L depletion in a cellular model for tuberous sclerosis causes a significant reduction in cell motility and invasiveness. Our data reveal that the two TFE3 isoforms exhibit partial redundancy and that the appearance of TFE3-L following prolonged stress potentially correlates with metastatic behaviors.

The V-SVZ niche is vital for adult neurogenesis in mammals, yet its regulation in humans remains poorly understood. Current models, including brain organoids, fail to replicate the unique cytoarchitecture of this niche, particularly the multiciliated ependymal cells, which are essential for its function and organization. Here, we utilize GEMC1 and MCIDAS to program human apical radial glial cells into ependymal cells, employing human brain organoids as a model. This approach induces premature ependymal cell differentiation and reorganization of the embryonic neurogenic niche, conferring characteristics of the human adult V-SVZ niche. Our findings highlight a molecular pathway that leads to ependymal cell generation and adult human V-SVZ niche reconstruction, providing a platform to study its development and function.