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Xist RNA initiates X inactivation as it spreads in cis across the chromosome. Here, we reveal a biophysical basis for its cis-limited diffusion. Xist RNA and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the chromosome. HNRNPK droplets pull on Xist and internalize the RNA. Once internalized, Xist induces a further phase transition and "softens" the HNRNPK droplet. Xist alters the condensate's deformability, adhesiveness, and wetting properties in vitro. Other Xist-interacting proteins are internalized and entrapped within the droplet, resulting in a concentration of Xist and protein partners within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts polycomb recruitment, and precludes the required mixing of chromosomal compartments for Xist's migration. Thus, we hypothesize that phase transitions in HNRNPK condensates allow Xist to locally concentrate silencing factors and to spread through internal channels of the HNRNPK-encapsulated chromosome., Competing Interests: Declaration of interests J.T.L. is a cofounder of Fulcrum Therapeutics, an advisor to Skyhawk Therapeutics, and a non-executive director of GSK. P.L. is a cofounder of NuPhase Therapeutics., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Inflammatory diseases are often chronic and recurrent, and current treatments do not typically remove underlying disease drivers 1 . T cells participate in a wide range of inflammatory diseases such as psoriasis 2 , Crohn's disease 3 , oesophagitis 4 and multiple sclerosis 5,6 , and clonally expanded antigen-specific T cells may contribute to disease chronicity and recurrence, in part by forming persistent pathogenic memory. Chronic rhinosinusitis and asthma are inflammatory airway diseases that often present as comorbidities 7 . Chronic rhinosinusitis affects more than 10% of the general population 8 . Among these patients, 20-25% would develop nasal polyps, which often require repeated surgical resections owing to a high incidence of recurrence 9 . Whereas abundant T cells infiltrate the nasal polyps tissue 10,11 , T cell subsets that drive the disease pathology and promote recurrence are not fully understood. By comparing T cell repertoires in nasal polyp tissues obtained from consecutive surgeries, here we report that persistent CD8 + T cell clones carrying effector memory-like features colonize the mucosal tissue during disease recurrence, and these cells characteristically express the tryptase Granzyme K (GZMK). We find that GZMK cleaves many complement components, including C2, C3, C4 and C5, that collectively contribute to the activation of the complement cascade. GZMK-expressing CD8 + T cells participate in organized tertiary lymphoid structures, and tissue GZMK levels predict the disease severity and comorbidities better than well-established biomarkers such as eosinophilia and tissue interleukin-5. Using a mouse asthma model, we further show that GZMK-expressing CD8 + T cells exacerbate the disease in a manner dependent on the proteolytic activity of GZMK and complements. Genetic ablation or pharmacological inhibition of GZMK after the disease onset markedly alleviates tissue pathology and restores lung function. Our work identifies a pathogenic CD8 + memory T cell subset that promotes tissue inflammation and recurrent airway diseases by the effector molecule GZMK and suggests GZMK as a potential therapeutic target., Competing Interests: Competing interests: H.Q. is a cofounder of Emergent Biomed Solutions, Ltd., (© 2025. The Author(s).)

Circular RNAs (circRNA) lack 5' or 3' ends; their unique covalently closed structures prevent RNA degradation by exonucleases. These characteristics provide circRNAs with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNAs. CircRNA levels are reportedly associated with certain human diseases, making them novel disease biomarkers and a noncanonical class of therapeutic targets. In this study, the endogenous circRNAs underlying the response to BNT162b2 mRNA vaccination were evaluated. To this end, peripheral blood samples were subjected to full-length sequencing of circRNAs via nanopore sequencing and transcriptome sequencing. Fifteen samples, comprising pre-, first, and second vaccination cohorts, were obtained from five healthcare workers with no history of SARS-CoV-2 infection or previous vaccination. A total of 4706 circRNAs were detected; following full-length sequencing, 4217 novel circRNAs were identified as being specifically expressed during vaccination. These circRNAs were enriched in the binding motifs of stress granule assemblies and SARS-CoV-2 RNA binding proteins, namely poly(A) binding protein cytoplasmic 1 (PABPC1), pumilio RNA binding family member 1 (PUM1), and Y box binding protein 1 (YBX1). Moreover, 489 circRNAs were identified as previously reported miRNA sponges. The differentially expressed circRNAs putatively originated from plasma B cells compared to circRNAs reported in human blood single-cell RNA sequencing datasets. The pre- and post-vaccination differences observed in the circRNA expression landscape in response to the SARS-CoV-2 BNT162b2 mRNA vaccine., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Human skin, as a sophisticated sensory organ, is able to detect subtle changes in ambient temperature. This thermosensory capability is primarily mediated by temperature-sensitive TRP channels expressed in both sensory neurons and keratinocytes. Among these, TRPV3, which responds to warm temperatures and plays a crucial role in various skin functions, is particularly notable. TRPV3 channels not only detect moderate warmth but are also sensitive to chemical ligands that evoke thermal sensations. The activation of TRPV3 by warm temperatures and compounds highlights its importance in the molecular mechanisms underlying skin thermosensation. This review mainly discusses the role of TRPV3, particularly its contribution to skin thermosensation and structural insights into its temperature sensitivity, providing an understanding of how TRPV3 modulates thermal perception at the molecular level., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025. Published by Elsevier Inc.)

Several mesenchymal cell populations are known to regulate intestinal stem cell (ISC) self-renewal and differentiation. However, the influences of signaling mediators derived from mesenchymal cells other than ISC niche factors on epithelial homeostasis remain poorly understood. Here, we show that host and microbial metabolites, such as taurine and GABA, act on PDGFRαhigh Foxl1high sub-epithelial mesenchymal cells to regulate their transcription. In addition, we found that CXCL12 produced from Foxl1high sub-epithelial mesenchymal cells induces epithelial cell cycle arrest through modulation of the mevalonate-cholesterol synthesis pathway, which suppresses tumor progression in ApcMin/+ mice. We identified that Foxl1high sub-epithelial cells highly express CXCL12 among colonic mesenchymal cells. Foxl1-cre; Cxcl12f/f mice showed an increased number of Ki67+ colonic epithelial cells. CXCL12-induced Ca2+ mobilization facilitated phosphorylation of AMPK in intestinal epithelial cells, which inhibits the maturation of SREBPs that are responsible for mevalonate pathway activation. Furthermore, Cxcl12 deficiency in Foxl1-expressing cells promoted tumor development in the small and large intestines of ApcMin/+ mice. Collectively, these results demonstrate that CXCL12 secreted from Foxl1high mesenchymal cells manipulates intestinal epithelial cell metabolism, which links to the prevention of tumor progression in ApcMin/+ mice., (© The Author(s) 2025. Published by Oxford University Press on behalf of The Japanese Society for Immunology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Revealing the structure stability and evolution of gold nanocrystals at the atomic scale is crucial to their versatile applications; however, the fundamental mechanism remains elusive due to the lack of in situ characterizations. In this work, the structural evolution of two types of Au nanobipyramids (Au NBPs) at elevated temperatures is monitored through in situ electron microscopy analysis, and there is a sharp distinction between their structure stability despite that they possess the same crystalline structure. Detailed material characterization reveals that the surface alloying of residual Ag with Au (customized Ag armor) can greatly inhibit the Au atom diffusion and contribute remarkably to the stability and surface-enhanced Raman scattering improvement. Moreover, the structure of the Au NBPs is further enhanced when the vulnerable tips are selectively coated with an oxide shell (Cu 2 O) to form a dumbbell-shaped nanostructure, which would undergo a completely different structure evolution at elevated temperatures.

Advancements in cryo-electron tomography (cryoET) allow the structure of macromolecules to be determined in situ, which is crucial for studying membrane protein structures and their interactions in the cellular environment. However, membranes are often highly curved and have a strong contrast in cryoET tomograms, which masks the signals from membrane proteins. These factors pose difficulties in observing and revealing the structures of membrane proteins in situ. Here, we report a membrane-flattening method and the corresponding software, MPicker, designed for the visualization, localization, and orientation determination of membrane proteins in cryoET tomograms. This method improves the visualization of proteins on and around membranes by generating a flattened tomogram that eliminates membrane curvature and reduces the spatial complexity of membrane protein analysis. In MPicker, we integrated approaches for automated particle picking and coarse alignment of membrane proteins for sub-tomogram averaging. MPicker was tested on tomograms of various cells to evaluate the method for visualizing, picking, and analyzing membrane proteins., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Despite the recent breakthrough in structure determination and prediction of proteins, the structural investigation of carbohydrates remains a challenge. Here, we report the cryo-EM analysis of a glycofibril found in the freshwater in the Tsinghua Lotus Pond. The fibril, which we name TLP-4, is made of a linear chain of tetrapeptide repeats coated with >4 nm thick glycans. In each repeat, two glycans are O-linked to a 3,4-dihydroxyproline and another glycan attaches to the adjacent Ser or Thr. The fibril structure is entirely maintained through glycan packing. Bioinformatic analysis confirms the conservation of the TLP-4 repeats across species, suggesting the existence of a large number of glycofibrils to be discovered. Our findings not only provide valuable insights into the structural roles of glycans in bio-assemblies but also demonstrate the potential of our recently formulated research strategy of CryoSeek to find bioentities and establish prototypes for structural studies of carbohydrates., Competing Interests: Competing interests statement:The authors declare no competing interest.

The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signalling pathway, which recognizes both pathogen DNA and host-derived DNA, has emerged as a crucial component of the innate immune system, having important roles in antimicrobial defence, inflammatory disease, ageing, autoimmunity and cancer. Recent work suggests that the regulation of cGAS-STING signalling is complex and sophisticated. In this Review, we describe recent insights from structural studies that have helped to elucidate the molecular mechanisms of the cGAS-STING signalling cascade and we discuss how the cGAS-STING pathway is regulated by both activating and inhibitory factors. Furthermore, we summarize the newly emerging understanding of crosstalk between cGAS-STING signalling and other signalling pathways and provide examples to highlight the wide variety of cellular processes in which cGAS-STING signalling is involved, including autophagy, metabolism, ageing, inflammation and tumorigenesis., Competing Interests: Competing interests: C.Z. has filed a patent application entitled “Function and application of SMPDL3A as a cGAMP-degrading enzyme”. Z.Z. declares no competing interests., (© 2025. Springer Nature Limited.)

RNA molecules function in numerous biological processes by folding into intricate structures. Here we present RASP v2.0, an updated database for RNA structure probing data featuring a substantially expanded collection of datasets along with enhanced online structural analysis functionalities. Compared to the previous version, RASP v2.0 includes the following improvements: (i) the number of RNA structure datasets has increased from 156 to 438, comprising 216 transcriptome-wide RNA structure datasets, 141 target-specific RNA structure datasets, and 81 RNA-RNA interaction datasets, thereby broadening species coverage from 18 to 24, (ii) a deep learning-based model has been implemented to impute missing structural signals for 59 transcriptome-wide RNA structure datasets with low structure score coverage, significantly enhancing data quality, particularly for low-abundance RNAs, (iii) three new online analysis modules have been deployed to assist RNA structure studies, including missing structure score imputation, RNA secondary and tertiary structure prediction, and RNA binding protein (RBP) binding prediction. By providing a resource of much more comprehensive RNA structure data, RASP v2.0 is poised to facilitate the exploration of RNA structure-function relationships across diverse biological processes. RASP v2.0 is freely accessible at http://rasp2.zhanglab.net/., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Immunometabolism is critical in the regulation of immunity and inflammation; however, the mechanism of preventing aberrant activation-induced immunopathology remains largely unclear. Here, we report that glyoxalase II (GLO2) in the glycolysis branching pathway is specifically downregulated by NF-κB signaling during innate immune activation via tristetraprolin (TTP)-mediated mRNA decay. As a result, its substrate S-D-lactoylglutathione (SLG) accumulates in the cytosol and directly induces D-lactyllysine modification of proteins. This nonenzymatic lactylation by SLG is greatly facilitated by a nearby cysteine residue, as it initially reacts with SLG to form a reversible S-lactylated thiol intermediate, followed by SN-transfer of the lactyl moiety to a proximal lysine. Lactylome profiling identifies 2255 lactylation sites mostly in cytosolic proteins of activated macrophages, and global protein structure analysis suggests that proximity to a cysteine residue determines the susceptibility of lysine to SLG-mediated D-lactylation. Furthermore, lactylation is preferentially enriched in proteins involved in immune activation and inflammatory pathways, and D-lactylation at lysine 310 (K310) of RelA attenuates inflammatory signaling and NF-κB transcriptional activity to restore immune homeostasis. Accordingly, TTP-binding site mutation or overexpression of GLO2 in vivo blocks this feedback lactylation in innate immune cells and promotes inflammation, whereas genetic deficiency or pharmacological inhibition of GLO2 restricts immune activation and attenuates inflammatory immunopathology both in vitro and in vivo. Importantly, dysregulation of the GLO2/SLG/D-lactylation regulatory axis is closely associated with human inflammatory phenotypes. Overall, our findings uncover an immunometabolic feedback loop of SLG-induced nonenzymatic D-lactylation and implicate GLO2 as a promising target for combating clinical inflammatory disorders., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Spermatogenesis is one of the most complex processes of cell differentiation and its failure is a major cause of male infertility. Therefore, a proper model that recapitulates spermatogenesis in vitro has been long sought out for basic and clinical research. Testis organ culture using the gas-liquid interphase method has been shown to support spermatogenesis in mice and rats. However, the conventional method using agarose gel has limitations including medium replacement efficiency and live imaging because agarose absorbs medium and is not transparent. To overcome this issue, we developed a new device using microporous membranes and oxygen-permeable materials. Mouse testes sandwiched between a microporous polyethylene terephthalate (PET) membrane on top and an oxygen-permeable 4-polymethyl-1-pentene polymer (PMP) membrane base maintained spermatogenesis over months. The chamber volume was minimized to 0.1% of the culture medium. Weekly time-lapse live imaging enabled us to observe transgenically fluorescent acrosome and nuclear shape formation throughout spermatogenesis. Finally, we obtained healthy fertile offspring from spermatozoa generated in our system. The device could be used not only for basic research to understand spermatogenesis but also for applied research, such as diagnosing and treating male infertility., Competing Interests: Declarations. Competing interests: Authors K.E., J.Y., and S.Y. were employed by Mitsui Chemicals, Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© 2024. The Author(s).)

Multiple sclerosis (MS) is a neurodegenerative disease characterized by demyelinated lesions in the brain and spinal cord. A few clinical studies using PET to image myelin in the brain have been performed, but none investigated the spinal cord. Because clinically relevant motor symptoms are primarily due to spinal cord damage, this translational study evaluated [ 11 C] N -methyl-4,4'-diaminostilbene (MeDAS) as a PET tracer for myelin imaging in the rat and human spinal cord. Methods: [ 11 C]MeDAS PET of the spinal cord was conducted in experimental autoimmune encephalomyelitis, lysophosphatidylcholine, and spinal cord injury animal models of focal demyelination. Then, 6 healthy controls and 11 MS patients were subjected to MRI and [ 11 C]MeDAS PET of the spinal cord between C5 and T6 vertebrae. Regions of interest covering 100%, 60%, and 40% of the diameter of the spinal canal were drawn, and tracer uptake was normalized to the activity in the blood pool, muscle, or injected dose per unit of body weight (SUV). Results: [ 11 C]MeDAS uptake was significantly reduced in spinal cord lesions in all animal models. In humans, tracer uptake was significantly higher in the cervical than the thoracic spinal cord, which corresponds well with the known physiologic rostral-caudal gradient in myelin density. MS patients had significantly lower [ 11 C]MeDAS uptake in the upper spinal cord (C5-T3) than did controls. The [ 11 C]MeDAS PET signal was inversely correlated with the presence of MS lesions in specific sections of the spinal cord. The best differentiation among regions with different myelin density was obtained when the smallest region of interest was used and spinal cord uptake was expressed as SUV. Conclusion: [ 11 C]MeDAS PET shows the potential to quantify myelin density in the spinal cord. It enables detection of physiologic differences in myelin density between spinal cord segments and between MS patients and healthy controls, which warrants further evaluation of this technique., (© 2025 by the Society of Nuclear Medicine and Molecular Imaging.)

Migrasomes, the vesicle-like membrane microstructures, arise on the retraction fibers (RFs), the branched nanotubules pulled out of cell plasma membranes during cell migration and shaped by membrane tension. Migrasomes form in two steps: a local RF bulging is followed by a protein-dependent stabilization of the emerging spherical bulge. Here, we addressed theoretically and experimentally the previously unexplored mechanism of bulging of membrane tubular systems. We assumed that the bulging could be driven by increases in membrane tension and experimentally verified this hypothesis in live-cell and biomimetic systems. We exposed RF-generating live cells to a hypotonic medium, which produced water flows into the cells and a related increase in the membrane tension. We observed the formation of migrasome-like bulges with a preferential location in the RF branching sites. Next, we developed a biomimetic system of three membrane tubules pulled out of a giant plasma membrane vesicle (GPMV), connected by a junction, and subjected to pulling forces controlled by the GPMV membrane tension. An abrupt increase in the GPMV tension resulted in the generation of migrasome-like bulges mainly in the junctions. To understand the physical forces behind these observations, we considered theoretically the mechanical energy of a membrane system consisting of a three-way tubular junction with emerging tubular arms subjected to membrane tension. Substantiating our experimental observations, the energy minimization predicted a tension increase to drive the formation of membrane bulges, preferably in the junction site, independently of the way of the tension application. We generalized the model to derive universal criteria of bulging in branched membrane tubules., Competing Interests: Declaration of interests L.Y. is the scientific founder of Migrasome Therapeutics Ltd. All other authors declare no competing interests related to this work., (Copyright © 2025 The Authors. Published by Elsevier Inc. All rights reserved.)

Anode-free solid-state batteries contain no active material at the negative electrode in the as-manufactured state, yielding high energy densities for use in long-range electric vehicles. The mechanisms governing charge-discharge cycling of anode-free batteries are largely controlled by electro-chemo-mechanical phenomena at solid-solid interfaces, and there are important mechanistic differences when compared with conventional lithium-excess batteries. This Perspective provides an overview of the factors governing lithium nucleation, growth, stripping and cycling in anode-free solid-state batteries, including mechanical deformation of lithium, the chemical and mechanical properties of the current collector, microstructural effects, and stripping dynamics. Pathways for engineering interfaces to maximize performance and extend battery lifetime are discussed. We end with critical research questions to pursue, including understanding behaviour at low stack pressure, tailoring interphase growth, and engineering current collectors and interlayers., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. Springer Nature Limited.)

Nucleic acid and protein co-condensates exhibit diverse morphologies crucial for fundamental cellular processes. Despite many previous studies that advanced our understanding of this topic, several interesting biophysical questions regarding the underlying molecular mechanisms remain. We investigated DNA and human transcription factor p53 co-condensates-a scenario where neither dsDNA nor the protein demonstrates phase-separation behavior individually. Through a combination of experimental assays and theoretical approaches, we elucidated: (1) the phase diagram of DNA-protein co-condensates at a certain observation time, identifying a phase transition between viscoelastic fluid and viscoelastic solid states, and a morphology transition from droplet-like to "pearl chain"-like co-condensates; (2) the growth dynamics of co-condensates. Droplet-like and "pearl chain"-like co-condensates share a common initial critical microscopic cluster size at the nanometer scale during the early stage of phase separation. These findings provide important insights into the biophysical mechanisms underlying multi-component phase separation within cellular environments., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Camera-based single-molecule techniques have emerged as crucial tools in revolutionizing the understanding of biochemical and cellular processes due to their ability to capture dynamic processes with high precision, high-throughput capabilities, and methodological maturity. However, the stringent requirement in photon number per frame and the limited number of photons emitted by each fluorophore before photobleaching pose a challenge to achieving both high temporal resolution and long observation times. In this work, we introduce MUFFLE, a supervised deep-learning denoising method that enables single-molecule FRET with up to 10-fold reduction in photon requirement per frame. In practice, MUFFLE extends the total number of observation frames by a factor of 10 or more, greatly relieving the trade-off between temporal resolution and observation length and allowing for long-term measurements even without the need for oxygen scavenging systems and triplet state quenchers., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) proteins are the minimal machinery required for vesicle fusion in eukaryotes. Formation of a highly stable four-helix bundle consisting of SNARE motif of these proteins, drives vesicle/membrane fusion involved in several physiological processes such as neurotransmission. Recycling/disassembly of the protein machinery involved in membrane fusion is essential and is facilitated by an AAA+ ATPase, N-ethylmaleimide sensitive factor (NSF) in the presence of an adapter protein, α-SNAP. Here we use single-molecule fluorescence spectroscopy approaches to elucidate the chain of events that occur during the disassembly of SNARE complex by NSF. Our observations indicate two major pathways leading to the sequential disassembly of the SNARE complex: one where a syntaxin separated intermediate state is observed before syntaxin disassembles first, and a second where Vamp disassembles from the other proteins first. These studies uncover two parallel sequential pathways for the SNARE disassembly by NSF along with a syntaxin separated intermediate that couldn't be observed otherwise., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Sesaminol is an organic compound which shows the strong antioxidant, anti-inflammatory, and neuroprotective properties. Sesaminol triglucoside (STG) is glycosylated form of sesaminol and abundantly exists in sesame seeds. However, typical β-glucosidases could not deglycosylate STG probably due to its bulky aglycone. PSTG1 and 2 are β-glucosidases lately isolated from Paenibacillis sp. KB0459 and have the capacity to deglycosylate STG. A recent report by Yanai et al. (J. Biochem. 2023; 174:335-344) revealed that the unique domain architecture of PSTG1. Apart from other β-glucosdasies in GH3 family, PSTG1 has novel accessary domain (domain 4) at the C-terminus. Domain 4 contributes the dimer formation and is located close to the active site. Interestingly, several hydrophobic residues are exposed, suggesting that this domain may recognize the hydrophobic aglycone of STG. The physiological functions of the non-catalytic domains in glyco-enzymes are sometimes overlooked. This paper shed light on the aglycone recognition by novel accessary domain., (© The Author(s) 2025. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.)

In a recent issue of Cell, Arribas et al. 1 and Pasquesi et al. 2 explore the phenomenon of transposable element (TE) exonization and its impact on proteomic and immune diversity, highlighting its potential role as a driver of evolutionary innovation., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Histone H3 monoaminylations at Gln5 represent an important family of epigenetic marks in brain that have critical roles in permissive gene expression 1-3 . We previously demonstrated that serotonylation 4-10 and dopaminylation 9,11-13 of Gln5 of histone H3 (H3Q5ser and H3Q5dop, respectively) are catalysed by transglutaminase 2 (TG2), and alter both local and global chromatin states. Here we found that TG2 additionally functions as an eraser and exchanger of H3 monoaminylations, including H3Q5 histaminylation (H3Q5his), which displays diurnally rhythmic expression in brain and contributes to circadian gene expression and behaviour. We found that H3Q5his, in contrast to H3Q5ser, inhibits the binding of WDR5, a core member of histone H3 Lys4 (H3K4) methyltransferase complexes, thereby antagonizing methyltransferase activities on H3K4. Taken together, these data elucidate a mechanism through which a single chromatin regulatory enzyme has the ability to sense chemical microenvironments to affect the epigenetic states of cells, the dynamics of which have critical roles in the regulation of neural rhythmicity., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Preimplantation embryonic development is orchestrated by dynamic changes in the proteome and transcriptome, regulated by mechanisms such as maternal-to-zygotic transition. Here, we employed label-free quantitative proteomics to comprehensively analyze proteome dynamics from germinal vesicle oocytes to blastocysts in mouse embryos. We identified 3490 proteins, including 715 consistently detected across all stages, revealing stage-specific changes in proteins associated with translation, protein modification, and mitochondrial metabolism. Comparison with transcriptomic data highlighted a low correlation between mRNA and protein levels, underscoring the significance of non-transcriptional regulatory mechanisms during early development. Additionally, we analyzed WD repeat-containing protein 74 (WDR74)-deficient embryos generated using CRISPR-Cas9 genome editing. WDR74, a pre-60S ribosome maturation factor, was found to be critical for ribosome biogenesis and cell division. Furthermore, WDR74 deficiency led to a significant reduction in ribosomal protein large subunit and impaired progression beyond the morula stage. Key ribosomal proteins such as ribosomal protein L24 (RPL24) and ribosomal protein L26 (RPL26), which influence cell division timing, were notably affected, while small subunit proteins remained largely unchanged. Taken together, our study demonstrates the utility of integrating genome editing with proteomic analysis to elucidate molecular mechanisms underlying early embryogenesis, and provides new insights into protein-level regulation of preimplantation development., (© 2025 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.)

The externalization of Phosphatidylserine (PS) from the inner surface of the plasma membrane to the outer surface of the plasma membrane is an emblematic event during apoptosis and serves as a potent "eat-me" signal for the efferocytosis of apoptotic cells. Although less well understood, PS is also externalized on live cells in the tumor microenvironment and on live virus-infected cells whereby it serves as an immune modulatory signal that drives tolerance and immune escape. Given the importance of PS in cancer immunology and immune escape, PS-targeting monoclonal antibodies have been characterized with promising immunotherapeutic potential. Here, we describe the cloning and characterization of a series of PS targeting antibodies and their potential use and utility in immuno-oncology., Competing Interests: Competing interests The authors have no financial conflicts to report. RBB is cofounder of Targeron Therapeutics, LLC, a biotechnology company that investigates novel PS-targeting therapeutics., (Copyright © 2025 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.)

Transcriptional regulation, which involves a complex interplay between regulatory sequences and proteins, directs all biological processes. Computational models of transcription lack generalizability to accurately extrapolate to unseen cell types and conditions. Here we introduce GET (general expression transformer), an interpretable foundation model designed to uncover regulatory grammars across 213 human fetal and adult cell types 1,2 . Relying exclusively on chromatin accessibility data and sequence information, GET achieves experimental-level accuracy in predicting gene expression even in previously unseen cell types 3 . GET also shows remarkable adaptability across new sequencing platforms and assays, enabling regulatory inference across a broad range of cell types and conditions, and uncovers universal and cell-type-specific transcription factor interaction networks. We evaluated its performance in prediction of regulatory activity, inference of regulatory elements and regulators, and identification of physical interactions between transcription factors and found that it outperforms current models 4 in predicting lentivirus-based massively parallel reporter assay readout 5,6 . In fetal erythroblasts 7 , we identified distal (greater than 1 Mbp) regulatory regions that were missed by previous models, and, in B cells, we identified a lymphocyte-specific transcription factor-transcription factor interaction that explains the functional significance of a leukaemia risk predisposing germline mutation 8-10 . In sum, we provide a generalizable and accurate model for transcription together with catalogues of gene regulation and transcription factor interactions, all with cell type specificity., Competing Interests: Competing interests: A provisional patent with application numbers 63/486,855 and PCT/US2024/017064 has been filed by Columbia University on the use of the method developed in this work to identify gene regulatory elements and alter gene regulation and expression; X.F. and R.R. are inventors on this patent. R.R. is a founder of Genotwin and a member of the SAB of Diatech Pharmacogenomics and Flahy. None of these activities are related to the work described in this manuscript., (© 2025. The Author(s).)

Bicelles, an artificial disk-shaped lipid bilayer, are commonly used for the structural and functional characterization of membrane-bound proteins in an environment similar to that in intracellular membranes. Because the dynamics of the lipids that constitute bicelles exert a significant impact on the structure and function of the inserted proteins, we investigated the mobility of lipid molecules in bicelles composed of DMPC (14:0 PC) and DHPC (06:0 PC) using solution NMR and MD calculations. 13 C R 1 relaxation experiments for the acyl groups demonstrated that increasing bicelle sizes limit the rotational diffusion of acyl chain H-C bonds in DMPC. Such a limited local motion around H-C bonds was also predicted in the MD simulations of DMPC bilayers with decreased area per lipid, indicating that the limited mobility of the hydrophobic core in larger bicelles is due to the tighter lipid packing. The downfield shifts of the 13 C NMR signals of the acyl groups supported the restricted mobility, corresponding to the conformational changes of the acyl chains from the flexible gauche rotamers to the less mobile trans rotamers with increase in bicelle size. These data suggest that larger bicelles pack lipids more densely, leading to increased trans conformation of the acyl chains and, consequently, less lipid motility, which can dynamically modulate the structure and function of membrane-bound proteins inserted into the bicelles., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Aberrant immune responses to viral pathogens contribute to pathogenesis, but our understanding of pathological immune responses caused by viruses within the human virome, especially at a population scale, remains limited. We analyzed whole-genome sequencing datasets of 6,321 Japanese individuals, including patients with autoimmune diseases (psoriasis vulgaris, rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), pulmonary alveolar proteinosis (PAP) or multiple sclerosis) and coronavirus disease 2019 (COVID-19), or healthy controls. We systematically quantified two constituents of the blood DNA virome, endogenous HHV-6 (eHHV-6) and anellovirus. Participants with eHHV-6B had higher risks of SLE and PAP; the former was validated in All of Us. eHHV-6B-positivity and high SLE disease activity index scores had strong correlations. Genome-wide association study and long-read sequencing mapped the integration of the HHV-6B genome to a locus on chromosome 22q. Epitope mapping and single-cell RNA sequencing revealed distinctive immune induction by eHHV-6B in patients with SLE. In addition, high anellovirus load correlated strongly with SLE, RA and COVID-19 status. Our analyses unveil relationships between the human virome and autoimmune and infectious diseases., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

The enzymes 3-methylcrotonyl-coenzyme A (CoA) carboxylase (MCC), pyruvate carboxylase and propionyl-CoA carboxylase belong to the biotin-dependent carboxylase family located in mitochondria. They participate in various metabolic pathways in human such as amino acid metabolism and tricarboxylic acid cycle. Many human diseases are caused by mutations in those enzymes but their structures have not been fully resolved so far. Here we report an optimized purification strategy to obtain high-resolution structures of intact human endogenous MCC, propionyl-CoA carboxylase and pyruvate carboxylase in different conformational states. We also determine the structures of MCC bound to different substrates. Analysis of MCC structures in different states reveals the mechanism of the substrate-induced, multi-element synergistic activation of MCC. These results provide important insights into the catalytic mechanism of the biotin-dependent carboxylase family and are of great value for the development of new drugs for the treatment of related diseases., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)

The growth plate is the primary site of longitudinal bone growth with chondrocytes playing a pivotal role in endochondral bone development. Chondrocytes undergo a series of differentiation steps, resulting in the formation of a unique hierarchical columnar structure comprising round, proliferating, pre-hypertrophic, and hypertrophic chondrocytes. Pre-hypertrophic chondrocytes, which exist in the transitional stage between proliferating and hypertrophic stages, are a critical cell population in the growth plate. However, the molecular basis of pre-hypertrophic chondrocytes remains largely undefined. Here, we employed scRNA-seq analysis on fluorescently labeled growth plate chondrocytes for their molecular characterization. Serine incorporator 5 (Serinc5) was identified as a marker gene for pre-hypertrophic chondrocytes. Histological analysis revealed that Serinc5 is specifically expressed in pre-hypertrophic chondrocytes, overlapping with Indian hedgehog (Ihh). Serinc5 represses cell proliferation and Col2a1 and Acan expression by inhibiting the transcriptional activity of Sox9 in primary chondrocytes. Chromatin profiling using ChIP-seq and ATAC-seq revealed an active enhancer of Serinc5 located in intron 1, with its chromatin status progressively activated during chondrocyte differentiation. Collectively, our findings suggest that Serinc5 regulates sequential chondrocyte differentiation from proliferation to hypertrophy by inhibiting Sox9 function in pre-hypertrophic chondrocytes, providing novel insights into the mechanisms underlying chondrocyte differentiation in growth plates., (© 2024 The Author(s). Journal of Cellular Physiology published by Wiley Periodicals LLC.)

Phospholipids are asymmetrically distributed in the plasma membrane (PM), with phosphatidylcholine and sphingomyelin abundant in the outer leaflet. However, the mechanisms by which their distribution is regulated remain unclear. Here, we show that transmembrane protein 63B (TMEM63B) functions as a membrane structure-responsive lipid scramblase localized at the PM and lysosomes, activating bidirectional lipid translocation upon changes in membrane curvature and thickness. TMEM63B contains two intracellular loops with palmitoylated cysteine residue clusters essential for its scrambling function. TMEM63B deficiency alters phosphatidylcholine and sphingomyelin distributions in the PM. Persons with heterozygous mutations in TMEM63B are known to develop neurodevelopmental disorders. We show that V44M, the most frequent substitution, confers constitutive scramblase activity on TMEM63B, disrupting PM phospholipid asymmetry. We determined the cryo-electron microscopy structures of TMEM63B in its open and closed conformations, uncovering a lipid translocation pathway formed in response to changes in the membrane environment. Together, our results identify TMEM63B as a membrane structure-responsive scramblase that controls PM lipid distribution and we reveal the molecular basis for lipid scrambling and its biological importance., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: N-Glycan branching modulates the diversity of protein functions. β1,4-N-acetylglucosaminyltransferase III (GnT-III or MGAT3) produces a unique GlcNAc branch, "bisecting GlcNAc", in N-glycans, and is involved in Alzheimer's disease and cancer. However, the 3D structure and catalytic mechanism of GnT-III are unclear. According to AlphaFold-based structure prediction, GnT-III likely contains two putative disordered segments, a long middle loop (Loop) and a C-terminal tail (Tail). We hypothesized that these segments play important roles in regulating the activity or intracellular behaviors of GnT-III., Methods: We expressed wild-type GnT-III (GnT-III-WT), GnT-III-Loop- and -Tail-deletion mutants in cells. Their in vitro catalytic activity and glycan biosynthesis in cells were examined using high-performance liquid chromatography, UDP-Glo glycosyltransferase assays, and glycomic analysis. Subcellular localization of WT and GnT-III mutants was investigated by immunostaining, and degradation rate and secretion were also examined., Results: The Loop-deletion mutant had higher in vitro and in cellulo activity than GnT-III-WT, indicating that Loop suppresses catalytic activity. In contrast, the Tail-deletion mutant showed weaker activity, increased ER localization, and faster degradation than GnT-III-WT, indicating that Tail is required for proper folding. In addition, deletion of Loop led to aberrant shedding of GnT-III, indicating that Loop contains the cleavage site or regulates GnT-III shedding., Conclusions: Loop and Tail of GnT-III play important roles in catalytic activity, folding and shedding., General Significance: Our results provide further understanding of the catalysis and shedding mechanisms of GnT-III and can help in the development of methods for modifying the levels of bisecting GlcNAc on glycoproteins and in cells., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Lipid mediator, palmitoylethanolamide (PEA) has recently attracted attention as a potential therapeutic option for various inflammatory autoimmune diseases. It has been reported that PEA exerts an inhibitory effect on inflammation triggered by PRRs, particularly Toll-like receptors expressed on myeloid antigen-presenting cells. However, the precise role of PEA in T cell development and function has not yet been elucidated. Here, we found that PEA suppressed the differentiation of Type 1 T helper (Th1) cells and Th17 cells, which are known to cause autoimmune diseases, as well as Th2 cells, which are associated with allergic diseases. This suppression occurs by inhibiting the expression of the master transcription factors crucial for their differentiation in vitro. Notably, PEA had no impact on the process of differentiating regulatory T cells, which play a crucial role in preventing the onset of autoimmune diseases. To further confirm the effect of PEA in vivo, we administered PEA to a Toxoplasma gondii infection model and an ovalbumin-induced allergic rhinitis model. Mice infected with T. gondii, in which Th1 responses are important for pathogen eradication, exhibited enhanced susceptibility. Mice with allergic rhinitis, where Th2 responses contribute to an exacerbation of symptoms, showed alleviated symptoms. Collectively, these findings suggest that PEA has potential applications as a new therapeutic agent for inflammatory autoimmune and allergic diseases based on excessive T cell activity., Competing Interests: Declaration of competing interest The authors have no competing financial interest to declare., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Mosaic analysis with double markers (MADM) is a powerful in vivo lineage tracing technique. It utilizes Cre recombinase-dependent interchromosomal recombination to restore the stable expression of two fluorescent proteins sparsely in individual dividing stem or progenitor cells and their progenies. Here, we describe the application of this technique for quantitative lineage analysis of radial glial progenitors in the developing mouse neocortex at the single-cell resolution., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Designing proteins with improved functions requires a deep understanding of how sequence and function are related, a vast space that is hard to explore. The ability to efficiently compress this space by identifying functionally important features is extremely valuable. Here we establish a method called EvoScan to comprehensively segment and scan the high-fitness sequence space to obtain anchor points that capture its essential features, especially in high dimensions. Our approach is compatible with any biomolecular function that can be coupled to a transcriptional output. We then develop deep learning and large language models to accurately reconstruct the space from these anchors, allowing computational prediction of novel, highly fit sequences without prior homology-derived or structural information. We apply this hybrid experimental-computational method, which we call EvoAI, to a repressor protein and find that only 82 anchors are sufficient to compress the high-fitness sequence space with a compression ratio of 10 48 . The extreme compressibility of the space informs both applied biomolecular design and understanding of natural evolution., Competing Interests: Competing interests: S.Z. and Z.M. have filed a patent application based on this work. The other authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)

DS-Cav1, SC-TM, and DS2 are distinct designer pre-fusion F proteins (pre-F) of respiratory syncytial virus (RSV) developed for vaccines. However, their immunogenicity has not been directly compared. In this study, we generated three recombinant vaccines using the chimpanzee adenovirus vector AdC68 to express DS-Cav1, SC-TM, and DS2. All three vaccines elicited robust serum binding and neutralizing antibodies following intramuscular priming and boosting. DS2 induced the strongest antibody responses, followed by SC-TM and DS-Cav1. DS2 also provided strong protection against live RSV challenge. Monoclonal antibodies (mAbs) isolated from long-lived antibody-secreting cells (ASCs) in the bone marrow six months post-immunization with AdC68-DS2 predominantly targeted site Ø as well as site II. One neutralizing antibody against site II, mAb60, conferred strong protection against live RSV infection in mice. These findings highlight the strong ability of the DS2 design in eliciting long-lived antibody responses and guide the development of next-generation RSV vaccines., Competing Interests: Competing interests: Patent application has been filed on a highly neutralizing antibody targeting RSV. L.Z., Y.Y., X.S. and Q.Z. are the inventors. The remaining authors declare no competing interests., (© 2024. The Author(s).)

Proteins without transmembrane domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol (GPI) molecules by the GPI transamidase (GPIT) complex. However, it remains poorly understood whether and how the GPIT complex affects primordial germ cell (PGC) development. In this study, we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk, both encoding essential GPIT complex subunits, resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably, a detailed analysis of filopodia in PGCs revealed the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC-specific rescue experiments demonstrated that both PGC and somatic cell-expressed Pigu are required for PGC migration. Furthermore, expression levels of PGC-specific genes decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence, we propose that the GPIT complex plays a critical role during PGC migration and development., (© The Author(s) 2024. Published by Oxford University Press on behalf of Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.)

Interstitial pneumonia (IP) is a refractory disease that causes severe inflammation and fibrosis in the interstitium of the lungs, often resulting in the development of lung cancer (LC) during treatment. Previous studies have demonstrated that the prognosis of LC complicated by IP is inferior to that of LC without IP. It is therefore of the utmost importance to gain a deeper understanding of the heterogeneity of such tumors. In the present study, we conducted spatial transcriptome analysis of squamous cell carcinoma arising from IP. The results suggested involvement of the glucocorticoid receptor pathway in treatment resistance. Immunostaining of squamous cell carcinoma specimens from patients with IP demonstrated that the tumors expressed NR3C1 to varying degrees. Furthermore, higher NR3C1 expression levels were associated with a significantly increased risk of recurrence. Our results point to a novel subtype of lung squamous cell carcinoma. Further analysis of the molecular mechanisms associated with this subtype may facilitate the development of novel diagnostic criteria and therapeutic approaches., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Psoriasis is a multifactorial disorder mediated by IL-17-producing T cells, involving immune cells and skin-constituting cells. Semaphorin 4A (Sema4A), an immune semaphorin, is known to take part in T helper type 1/17 differentiation and activation. However, Sema4A is also crucial for maintaining peripheral tissue homeostasis and its involvement in skin remains unknown. Here, we revealed that while Sema4A expression was pronounced in psoriatic blood lymphocytes and monocytes, it was downregulated in the keratinocytes of both psoriatic lesions and non-lesions compared to controls. Imiquimod application induced more severe dermatitis in Sema4A knockout (KO) mice compared to wild-type (WT) mice. The naïve skin of Sema4A KO mice showed increased T cell infiltration and IL-17A expression along with thicker epidermis and distinct cytokeratin expression compared to WT mice, which are hallmarks of psoriatic non-lesions. Analysis of bone marrow chimeric mice suggested that Sema4A expression in keratinocytes plays a regulatory role in imiquimod-induced dermatitis. The epidermis of psoriatic non-lesion and Sema4A KO mice demonstrated mTOR complex 1 upregulation, and the application of mTOR inhibitors reversed the skewed expression of cytokeratins in Sema4A KO mice. Conclusively, Sema4A-mediated signaling cascades can be triggers for psoriasis and targets in the treatment and prevention of psoriasis., Competing Interests: MK, HK, YM, AT, KY, YN, NO, MT, KT, TK, MW, AK, MF, RW No competing interests declared, SN, SM affiliated with Maruho Co. as an employee, but has declared no conflicts of interest related to this research, (© 2024, Kume et al.)

Exceptionally diverse type V CRISPR-Cas systems provide numerous RNA-guided nucleases as powerful tools for DNA manipulation. Two known Cas12e nucleases, DpbCas12e and PlmCas12e, are both effective in genome editing. However, many differences exist in their in vitro dsDNA cleavage activities, reflecting the diversity in Cas12e's enzymatic properties. To comprehensively understand the Cas12e family, we identify and characterize six unreported Cas12e members that vary in their CRISPR-locus architectures, PAM preferences, and cleavage efficacies. Interestingly, among all variants, PlmCas12e exhibits the most robust trans-cleavage activity and the lowest salt sensitivity in cis-cleavage. Further structural comparisons reveal that the unique NTSB domain in PlmCas12e is beneficial to DNA unwinding at high salt concentrations, while some NTSB-lacking Cas12e proteins rely on positively charged loops for dsDNA unwinding. These findings demonstrate how divergent evolution of structural elements shapes the nuclease diversity within the Cas12e family, potentially contributing to their adaptations to varying environmental conditions., Competing Interests: Competing interests: J.J.G.L., S.Z., and D.L. have submitted patent applications to the China patent office pertaining to the following aspects of this work: (1) DNA manipulating tools using CRISPR-LesCas12e, -VemCas12e, -HrbCas12e, and -CkbCas12e systems. Applicant: Tsinghua University. Status: Granted. Application number: 2022106204929 [P]. (2) DNA manipulating tools using CRISPR-OpbCas12e and -Plm2Cas12e systems. Applicant: Tsinghua University. Status: Filed. The remaining authors declare no competing interests., (© 2024. The Author(s).)

Micropapillary adenocarcinoma (MPC) is an aggressive histological subtype of lung adenocarcinoma (LUAD). MPC is composed of small clusters of cancer cells exhibiting inverted polarity. However, the mechanism underlying its formation is poorly understood. Here we show that hypoxia is involved in MPC formation. Hypoxia induced the formation of MPC-like structures (MLSs) in a three-dimensional culture system using A549 human LUAD cells, and HIF-1α was indispensable for MLS formation. RNA sequencing analysis demonstrated that A549 cells forming MLSs exhibited a gene expression signature similar to that of lung MPC. Moreover, MLS formation enhanced the resistance of A549 cells to natural killer cell cytotoxicity. Our findings suggest that hypoxia drives lung MPC formation through HIF-1α and that immune escape from natural killer cells might underlie the aggressiveness of MPC., Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethical approval: All experimental protocols involving human specimens were approved by the Ethics Review Board of the Graduate School of Medicine, Osaka University (approval no. 15234) and carried out in accordance with the committee’s guidelines and regulations. The study was performed in accordance with the Declaration of Helsinki., (© 2024. The Author(s).)

The immune system exhibits spatial diversity in in vivo tissues. Immune cells are strategically distributed within tissues to maintain the organ integrity. Advanced technologies such as intravital imaging and spatial transcriptomics have revealed the spatial heterogeneity of immune cell distribution and function within organs such as the liver, kidney, intestine, and lung. In addition, these technologies visualize nutrient and oxygen environments across tissues. Recent spatial analyses have suggested that a functional immune niche is determined by interactions between immune and non-immune cells in an appropriate nutrient and oxygen environment. Understanding the spatial communication between immune cells, environment, and surrounding non-immune cells is crucial for developing strategies to control immune responses and effectively manage inflammatory diseases., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Japanese Society for Immunology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Mycobacterium tuberculosis causes human tuberculosis. As mycobacteria are protected by thick lipid cell wall, humans have developed immune responses against diverse mycobacterial lipids. Most of these immunostimulatory lipids are known as adjuvants acting through innate immune receptors, such as C-type lectin receptors. Although a few mycobacterial lipid antigens activate unconventional T cells, antigenicity of most adjuvantic lipids are unknown. Here, we identified that trehalose monomycolate (TMM), an abundant mycobacterial adjuvant, activates human T cells bearing a unique ɑβTCR. This recognition was restricted by CD1b, a monomorphic antigen-presenting molecule conserved in primates but not mice. Single-cell TCR-RNA sequencing using newly established CD1b-TMM tetramers revealed that TMM-specific T cells are present as CD4+ effector memory T cells in the periphery of uninfected donors, but express IFNγ, TNF and anti-mycobacterial effectors upon TMM stimulation. TMM-specific T cells are detected in cord blood and PBMCs of non-BCG-vaccinated donors, but are expanded in active tuberculosis patients. A cryo-electron microscopy study of CD1b-TMM-TCR complexes revealed unique antigen recognition by conserved features of TCRs, positively-charged CDR3ɑ and long CDR3β regions. These results indicate that humans have a commonly-shared and pre-formed CD4+ T cell subset recognizing a typical mycobacterial adjuvant as an antigen. Furthermore, the dual role of TMM justifies reconsideration of the mechanism of action of adjuvants.

Excited-state intramolecular proton transfer (ESIPT) molecules are promising fluorophores for various applications including bioimaging, sensing, and optoelectronic devices. Particularly, their self-absorption-free fluorescence properties would make them a perfect choice as emissive materials for organic light-emitting diodes (OLEDs). Nevertheless, to become effective emitters some of their properties need to be altered by structural modifications. Herein, we design and synthesize a series of new ESIPT molecules (2PImBzP, 2ImBzP, and 2FImBzP) by functionalization of imidazole-phenol-based ESIPT cores with electron-deficient benzo[d]thiazole and various ambipolar imidazole moieties (1-phenyl-1H-phenanthro[9,10-d]imidazole (PIm), 1,4,5-triphenyl-1H-imidazole (Im), and (4,5-bis(4-fluorophenyl)-1-phenyl-1H-imidazole (FIm)), respectively. Each molecule displays a complete ESIPT process with intense green emissions from a pure keto form and high solid-state photoluminescence quantum yields (Φ PL ) of 65-80 %. These fluorophores with superior thermal stability and balanced charge carrier mobility are effectively employed as non-doped emitters in OLEDs. The non-doped devices emit greenish lights with high brightness, high current efficiency (CE) (10.95-17.66 cd A -1 ), and low turn-on voltages (2.8-2.9 V). The electroluminescence purely originates from the emission of the keto tautomer of the emissive layers. Specifically, the 2PImBzP-based non-doped OLED stands out by achieving a remarkable brightness of 56,220 cd m -2 , a CE of up to 17.66 cd A -1 , and an impressive external quantum efficiency (EQE) of 5.65 % with a slight efficiency roll-off., (© 2024 Wiley-VCH GmbH.)

The spatial propagation of neuronal activity within neuronal circuits, which is associated with brain functions, such as memory and learning, is regulated by external stimuli. Conventional external stimuli, such as electrical inputs, pharmacological treatments, and optogenetic modifications, have been used to modify neuronal activity. However, these methods are tissue invasive, have insufficient spatial resolution, and cause irreversible gene modifications. To establish neuronal stimulation with less invasiveness and higher spatial resolution, we propose and demonstrate single-neuron stimulation using a focused femtosecond laser. Fluorescence Ca 2+ imaging and microelectrode array recordings of extracellular potentials revealed Ca 2+ influx into the target neuron and high-frequency electrical responses after laser irradiation. These results indicate that femtosecond laser-induced neuronal electrical activity has a greater number of electrical spikes, lasts longer after stimulation, and propagates to a region more distant from the target neuron compared with the properties evoked by electrical stimulation. Focused femtosecond laser-induced stimulation can be a promising tool for stimulating single neurons in neuronal networks., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

(1) Background: Fetal chromosomal examination is a critical component of modern prenatal testing. Traditionally, maternal serum biomarkers such as free β-human chorionic gonadotropin (Free β-HCG) and pregnancy-associated plasma protein A (PAPPA) have been employed for screening, achieving a detection rate of approximately 90% for fetuses with Down syndrome, albeit with a false positive rate of 5%. While amniocentesis remains the gold standard for the prenatal diagnosis of chromosomal abnormalities, including Down syndrome and Edwards syndrome, its invasive nature carries a significant risk of complications, such as infection, preterm labor, or miscarriage, occurring at a rate of 7 per 1000 procedures. Beyond Down syndrome and Edwards syndrome, other chromosomal abnormalities, such as trisomy of chromosomes 9, 16, or Barr bodies, pose additional diagnostic challenges. Non-invasive prenatal testing (NIPT) has emerged as a powerful alternative for fetal genetic screening by leveraging maternal blood sampling. However, due to the extremely low abundance of fetal cells in maternal circulation, NIPT based on fetal cells faces substantial technical challenges. (2) Methods: Fetal nucleated red blood cells (FnRBCs) were first identified in maternal circulation in a landmark study published in The Lancet in 1959. Due to their fetal origin and presence in maternal peripheral blood, FnRBCs represent an ideal target for non-invasive prenatal testing (NIPT). In this study, we introduce a novel self-assembled cell array (SACA) chip system, a microfluidic-based platform designed to efficiently settle and align cells into a monolayer at the chip's base within five minutes using lateral flow dynamics and gravity. This system is integrated with a fully automated, multi-channel fluorescence scanning module, enabling the real-time imaging and molecular profiling of fetal cells through fluorescence-tagged antibodies. By employing a combination of Hoechst+/CD71+/HbF+/CD45- markers, the platform achieves the precise enrichment and isolation of FnRBCs at the single-cell level from maternal peripheral blood. (3) Results: The SACA chip system effectively reduces the displacement of non-target cells by 31.2%, achieving a single-cell capture accuracy of 97.85%. This isolation and enrichment system for single cells is well suited for subsequent genetic analysis. Furthermore, the platform achieves a high purity of isolated cells, overcoming the concentration detection limit of short tandem repeat (STR) analysis, demonstrating its capability for reliable non-invasive prenatal testing. (4) Conclusions: This study demonstrates that the SACA chip, combined with an automated image positioning system, can efficiently isolate single fetal nucleated red blood cells (FnRBCs) from 50 million PBMCs in 2 mL of maternal blood, completing STR analysis within 120 min. With higher purification efficiency compared to existing NIPT methods, this platform shows great promise for prenatal diagnostics and potential applications in other clinical fields.

A synthetic method was developed for the generation of a quaternary carbon center in carbonyl compounds. This innovative process involved the reaction of α-thiolate lactones and cycloalkanones with two equivalents of arynes in acetonitrile to give α,α-diarylated products in 63-85% yields at 25 °C. The reaction unfolds through an unconventional domino process, encompassing sequential 1,2-elimination, 1,2-nucleophilic addition, 1,4-proton transfer, the second 1,2-nucleophilic addition, interrupted Pummerer rearrangement, intramolecular spirocyclization, and sulfonium ring-opening. The potential of this "single-flask" reaction was systematically investigated and found well-suited to generate diarylated carbonyl compounds, incorporating naphthalene, pyridine, quinoline, or isoquinoline rings adorned with various substituents.

PIEZO1 is a mechanically activated cation channel that undergoes force-induced activation and inactivation. However, its distinct structural states remain undefined. Here, we employed an open-prone PIEZO1-S2472E mutant to capture an intermediate open structure. Compared with the curved and flattened structures of PIEZO1, the S2472E-Intermediate structure displays partially flattened blades, a downward and rotational motion of the top cap, and a spring-like compression of the linker connecting the cap to the pore-lining inner helix. These conformational changes open the cap gate and the hydrophobic transmembrane gate, whereas the intracellular lateral plug gate remains closed. The flattened structure of PIEZO1 with an up-state cap and closed cap gate might represent an inactivated state. Molecular dynamics (MD) simulations of ion conduction support the closed, intermediate open, and inactivated structural states. Mutagenesis and electrophysiological studies identified key domains and residues critical for the mechanical activation of PIEZO1. These studies collectively define the distinct structural states and gating transitions of PIEZO1., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The recruitment of T lymphocytes holds great potential for suppressing the most aggressive glioblastoma (GBM) recurrence with immunotherapy. However, the phenomenon of immune privilege and the generally low immunogenicity of vaccines often reduce the presence of lymphocytes within brain tumors, especially in brain tumor recurrence clusters. In this study, an implantable self-cascading catalytic therapy and antigen capture scaffold (CAS) that can boost catalytic therapy efficiency at post-surgery brain tumor and capture the antigens via urethane-polyethylene glycol-polypropylene glycol (PU-EO-PO) segments are developed for postoperative brain immunotherapy. The CAS consists of 3D-printed elastomers modified with iron (Fe 2+ ) metal-organic frameworks (MOFs, MIL88) and acts as a programmed peroxide mimic in cancer cells to initiate the Fenton reaction and sustain ROS production. With the assistance of chloroquine (CQ), autophagy is inhibited through lysosome deacidification, which interrupts the self-defense mechanism, further enhances cytotoxicity, and releases antigens. Then, CAS containing PU-EO-PO groups acts as an antigen depot to detain autologous tumor-associated antigens to dendritic cells maturation and T cell augments for sustained immune stimulation. CAS enhanced the immune response to postoperative brain tumors and improved survival through brain immunotherapy., (© 2024 Wiley‐VCH GmbH.)

The Gram-negative bacteria Bordetella pertussis, B. parapertussis, and B. bronchiseptica cause respiratory diseases in various mammals. They share the BvgAS two-component system, which regulates the phenotypic conversion between the virulent Bvg + and avirulent Bvg - phases. In the BvgAS system, the sensor kinase BvgS senses environmental cues and transduces a phosphorelay signal to the response regulator BvgA, which leads to the expression of Bvg + phase-specific genes, including virulence factor genes. Bacteria grown at 37°C exhibit the Bvg + phenotype. In contrast, at lower than 26°C or in the presence of modulators, such as MgSO 4 and nicotinic acid, the BvgAS system is inactivated, leading bacteria to the avirulent Bvg - phase. Therefore, effective modulators are expected to provide a therapeutic measure for Bordetella infection; however, no such modulators are currently available, and the mechanism by which modulators inactivate the BvgAS system is poorly understood. In the present study, we identified lonidamine as a novel modulator after screening an FDA-approved drug library using bacterial reporter systems with the Bvg + -specific and Bvg - -specific promoters. Lonidamine directly bound to the VFT2 domain of BvgS and inactivated the BvgAS system at concentrations as low as 50 nM, which was at least 2000- to 20,000-fold lower than the effective concentrations of known modulators. Lonidamine significantly reduced the adherence of B. pertussis to cultured cells but unexpectedly exacerbated bacterial colonization of the mouse nasal septum. These results provide insights into the structural requirements for BvgAS modulators and the role of Bvg phenotypes in the establishment of infection., (© 2024 The Author(s). Microbiology and Immunology published by The Societies and John Wiley & Sons Australia, Ltd.)