EMBO Reports最新文献

The immune checkpoint molecule, programmed cell death 1 (PD-1), critically regulates T-cell activation upon binding PD-L1 or PD-L2, making it a key target in cancer immunotherapy. Although extensively studied, the molecular mechanism of the inhibitory function of PD-1 remains incompletely understood. Using the biomembrane force probe (BFP), we measure catch-slip bond behavior between PD-1 and PD-L1/PD-L2 under force. Steered molecular dynamics (SMD) simulation reveals a force-induced bound state distinct from the force-free state observed in solved complex structures. Disrupting interactions that stabilize either state weakens the catch bond, and diminishes the inhibitory function of PD-1. Interestingly, soluble forms of PD-L1/PD-L2 compete with their surface-bound counterparts and attenuate PD-1-mediated T-cell inhibition, suggesting that soluble PD-1 ligands could potentially serve as anti-PD-1 drugs. Tumor growth studies using a gain of function mutant based on the catch-bond mechanism confirm the anti-cancer activity of soluble PD-L1. Our findings highlight that mechanical force governs the inhibitory function of PD-1 and suggest that PD-1 acts as a mechanical sensor in T-cell suppression. Thus, mechanical regulation should be considered when designing PD-1 blocking therapies.

Maternal effect genes (MEGs) produce factors that accumulate in oocytes and play critical roles in embryo development. Mutations of MEGs are frequently linked to reproductive and congenital disorders. The majority of identified mammalian MEGs encode epigenetic factors and RNA regulators. Here, we identify a MEG encoding the transcription factor Thanatos-associated protein 1 (Thap1). Thap1 is highly expressed in mouse oocytes and early embryos. Oocyte-specific deletion of Thap1 results in delayed progression of mouse embryos from the 1-cell to the 2-cell stage and 1-2-cell arrest, accompanied by defective zygotic genome activation (ZGA) and strongly impaired female fertility. Mechanistically, THAP1 activates a critical subset of genes in oocytes, including Rrm1, which produces ribonucleotide reductase required for generating deoxynucleotide triphosphates (dNTPs). Low-input metabolome profiling across 7 stages during the oocyte-to-embryo transition shows gradual, THAP1-dependent dNTP accumulation that peaks in MII oocytes. Overexpression of Rrm1 in zygotes almost fully restores the 2-cell progression and ZGA in Thap1 maternal-knockout embryos. Our findings identify THAP1 as a key maternal effector critical for the earliest stage of mammalian development.

Regulation of RNA polymerase II (Pol II) transcription is closely associated with cell proliferation. However, it remains unclear how the Pol II transcription program is rewired in cancer to promote uncontrolled growth. Here, we find that expression of NELFCD, a known negative transcription elongation factor, is upregulated in colorectal tumors. Auxin-dependent protein degradation of NELF-C in combination with nascent transcript sequencing demonstrates a direct role of NELF-C on Pol II transcription in this cancer. Strikingly, we demonstrate that the acute loss of NELF-C protein globally redistributes termination factors and perturbs Pol II transcription termination. These changes drive pervasive Pol II transcription into DNA replication zones, leading to transcription-replication conflict that may block the cell cycle in G1 or early S phase. Our findings reveal a previously unrecognized role of NELF in transcription termination and highlight NELF as a potential therapeutic target in colorectal cancer.

Progenitor proliferation during neurodevelopment requires tight coordination of epigenetic regulation and metabolism. However, the crosstalk between these processes remains poorly understood. To investigate this, we examine in neural stem cells the role of PHF8, a histone demethylase whose mutations are linked to Siderius-Hamel syndrome, a rare neurodevelopmental disorder. Through an integrated multi-omics approach - combining transcriptomics, epigenomics, and metabolomics - we identify PHF8 as a key driver of the serine biosynthesis pathway, safeguarding the intracellular serine pool essential for neural progenitor proliferation. PHF8 fine-tunes chromatin accessibility at promoters of metabolic genes, ensuring their activation during development. Loss of PHF8 disrupts amino acid metabolism, blocks autophagy, and hinders vesicle formation. Ultimately PHF8 depletion leads to replication defects, DNA damage, and proliferation arrest. In vivo, PHF8 deficiency in mouse embryos halts neurogenesis, progenitor expansion, and neuron generation in the developing brain. These findings identify PHF8 as a key molecular link between chromatin regulation, metabolic control, and neural development, offering new insights into the epigenetic basis of neurodevelopmental and metabolic disorders.

Gim3 is an evolutionarily conserved component of the prefoldin chaperone complex, involved in protein folding. We previously found that GIM3 genetically interacts with many de novo mutations in Saccharomyces cerevisiae. Removing GIM3 from mutagenized S. cerevisiae cells significantly affected the fitness effect of mutations. This indicates that Gim3 might change the evolutionary impact of de novo mutations by either buffering (hiding) or potentiating (increasing) their phenotypic effects, depending on the environmental or genetic context. Here, we investigated Gim3's role in shaping the evolutionary fate of de novo mutations under fluconazole stress, an antifungal drug used to combat fungal infections. Applying both strong and moderate fluconazole stress in the presence or absence of GIM3 revealed that Gim3 potentiates fluconazole susceptibility (resistance and tolerance) by enabling mutations to have immediate phenotypic effects. Deleting GIM3 reduced growth in fluconazole in most mutants, indicating that GIM3 could be a promising target for new antifungal therapies against drug-resistant infections. Importantly, Gim3 also modulates fluconazole susceptibility of the fungal pathogen Nakaseomyces glabratus, further highlighting Gim3's role in fluconazole resistance and tolerance.

Granulomatosis with polyangiitis is a life-threatening systemic vasculitis, characterised by anti-neutrophil cytoplasmic autoantibodies (ANCA) most commonly against proteinase 3 (PR3), a protease expressed intracellularly and on the surface of neutrophils. Most cell surface PR3 is bound to the receptor CD177; however, the molecular mechanism of the interactions is not well understood. Here, we present crystal structures of CD177 in complex with PR3 and unliganded CD177. We describe a mainly hydrophobic binding interface between PR3 and CD177, involving the first two Ly6/uPAR (LU) domains of CD177. These form a globular structure which is connected to downstream domains via a flexible linker. Using a panel of PR3-ANCA-positive patient samples, we show that a significant proportion of ANCAs target the CD177-binding site of PR3 in these samples. Structure-guided mutation of the CD177-binding site on PR3 is effective in reducing PR3-ANCA binding. The results demonstrate that the CD177-binding surface of PR3 harbours a major PR3-ANCA epitope, and that the extent of binding to this surface varies between different patients.

Telomeres cap the extremities of linear chromosomes and prevent their detection as DNA damage. Telomere uncapping poses a profound threat to genome integrity, yet the immediate consequences of transient uncapping remain unclear. In Saccharomyces cerevisiae, the Cdc13-Stn1-Ten1 complex limits resection, preventing DNA damage checkpoint activation. Here, using the temperature-sensitive cdc13-1 allele, we demonstrate that transient telomere uncapping rapidly induces extensive genomic rearrangements despite a functional DNA damage checkpoint. Two distinct rearrangement signatures are observed in surviving cells: recombination of the subtelomeric region mostly involving the Y' elements, and massively elongated telomeres up to 10 kb, a ~ 30-fold increase. Long-read sequencing evidences Y' element losses/amplifications, terminal duplications, and telomeric-circle-driven amplifications of telomere repeats. Rearrangements unfold over multiple generations and require the homologous recombination factor Rad52, the Polδ subunit Pol32, and partially Rad51 and Rad59. Remarkably, survivors with elongated telomeres demonstrate a robust Rad52-dependent resistance to subsequent telomere uncapping. Our findings provide novel insights into the consequences of transient telomere uncapping for genome stability, a process that might contribute to subtelomere and telomere dynamics and evolution.