Search

Alternative splicing contributes to complex traits, but whether this differs in trait-relevant cell types across diverse genetic ancestries is unclear. Here we describe cell-type-specific, sex-biased and ancestry-biased alternative splicing in ~1 M peripheral blood mononuclear cells from 474 healthy donors from the Asian Immune Diversity Atlas. We identify widespread sex-biased and ancestry-biased differential splicing, most of which is cell-type-specific. We identify 11,577 independent cis-splicing quantitative trait loci (sQTLs), 607 trans-sGenes and 107 dynamic sQTLs. Colocalization between cis-eQTLs and trans-sQTLs revealed a cell-type-specific regulatory relationship between HNRNPLL and PTPRC. We observed an enrichment of cis-sQTL effects in autoimmune and inflammatory disease heritability. Specifically, we functionally validated an Asian-specific sQTL disrupting the 5' splice site of TCHP exon 4 that putatively modulates the risk of Graves' disease in East Asian populations. Our work highlights the impact of ancestral diversity on splicing and provides a roadmap to dissect its role in complex diseases at single-cell resolution., Competing Interests: Competing interests: X.J. is an employee of BGI Research. Y. Tong is undertaking a PhD scholarship partially supported by BGI Research. The other authors declare no competing interests., (© 2024. The Author(s).)

Escherichia coli O111 is a critical pathogenic E. coli serotype that causes severe, potentially fatal complications. Despite its reported variation, only one structure of the O-antigen polysaccharide from E. coli O111 has been reported. Here, a substructure of the O-antigen from E. coli O111 was characterized using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and NMR analysis. MALDI glycotyping revealed differing O-antigen repeating unit masses of Δm/z 787 and 828 in the E. coli strains and lipopolysaccharides from the O111 serogroup. This variation was caused by the replacement of the hexose residue with hexosamine in the repeating units, which was further confirmed by LIFT-TOF/TOF analysis. Structural elucidation of the O111 substructure by NMR analysis further demonstrated replacement of the hydroxyl group with an N-acetyl group on the terminal glucose residue of the O-antigen pentasaccharide repeating unit. To our knowledge, this study is the first to provide a detailed structural analysis of a new O-antigen substructure from the E. coli O111 serogroup., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Hiroshi Hinou reports financial support, administrative support, and equipment, drugs, or supplies were provided by Hokkaido University, Japan. Hiroshi Hinou and Shogo Urakami reports financial support was provided by Japan Society for the Promotion of Science, Japan. June Chelyn Lee reports financial support was provided by Government of Japan Ministry of Education Culture Sports Science and Technology. June Chelyn Lee reports a relationship with Ministry of Health Malaysia that includes: employment. If there are other authors, they 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.)

Background: Subarachnoid hemorrhage (SAH) can lead to acute or delayed cerebral ischemia. Recent findings have revealed that spasm of microvessels, called microvasospasm, may contribute to SAH-related cerebral ischemia, and perivascular inflammation is considered important in the development of microvasospasms. However, owing to the difficulty in investigating the dynamics of vascular and perivascular events, little is known about the mechanisms underlying microvasospasms., Methods: We established an experimental system aiming to investigate the vascular and perivascular pathology of SAH by combining a SAH mouse model with intravital 2-photon imaging. SAH was induced by intracisternal blood injection, and the distribution of erythrocytes, neutrophil behavior, and morphological changes in the pial arterioles were analyzed over time by 2-photon microscopy imaging. To further explore the role of neutrophils and neutrophil extracellular traps (NETs) in microvasospasm, we performed neutrophil depletion by intraperitoneal administration of neutrophil-specific antibody or NETs removal by intracisternal administration of DNase., Results: Erythrocytes were immediately distributed in the perivascular space of the arterioles after SAH induction; neutrophils intensively infiltrated the perivascular space within 2 days and subsequently showed NETosis; and pial arterioles in the same region developed pearl-string-like microvasospasms in the subacute phase. Neutrophil depletion significantly reduced the number of microvasospasms. Furthermore, the removal of perivascular NETs drastically reduced microvasospasms., Conclusions: By establishing a unique experimental system, we demonstrated that perivascular NETs could be a new therapeutic target for microvasospasms., Competing Interests: None.

Voltage-gated sodium (Na v ) channels are crucial in transmitting action potentials in neurons. The tetrodotoxin-resistant subtype Na v 1.8 is predominantly expressed in the peripheral nervous system, offering a unique opportunity to design selective inhibitors for pain relief. A number of compounds have been reported to specifically block Na v 1.8. Among these, VX-548 is already in regulatory review for the treatment of moderate-to-severe acute pain and holds the promise to be the first non-opioid pain killer over the past twenty years. Recent structural studies using cryogenic electron microscopy (cryo-EM) and structure-based predictive modeling have provided unprecedented insights into the structural pharmacology of Na v 1.8. In this review, we summarize the latest developments in Na v 1.8-selective inhibitors, focusing on the druggable sites and mechanisms that confer subtype specificity. These structural insights highlight the potential for Na v 1.8 inhibitors to deliver non-addictive pain management, thus illuminating the avenue to next-generation analgesic development., 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 Ltd. All rights reserved.)

Competing Interests: Competing interests: The authors declare no competing interests.

Incomplete Freund's adjuvant (IFA) has long been used to trigger autoimmune diseases in animal models, such as experimental autoimmune encephalitis and collagen-induced arthritis. However, the molecular mechanisms that control CD4 T cell effector functions and lead to the development of autoimmune diseases are not well understood. A self-antigen and heat-killed Mycobacterium tuberculosis emulsified in IFA augmented the activation of CD4 T cells, leading to the differentiation of pathogenic CD4 T cells in the draining lymph nodes. In contrast, IFA emulsification did not elicit Foxp3 + regulatory T cell expansion. We found that pathogenic Th1 cells expressed miR-147-3p, which targets multiple genes to affect T cell function. Finally, miR-147-3p expressed in CXCR6 + SLAMF6 - Th1 cells was required for the onset of neurological symptoms through the control of CXCR3 expression. Our findings demonstrate that miR-147-3p expressed in pathogenic CD4 T cells regulates the migratory potential in peripheral tissues and impacts the development of autoimmune diseases., Competing Interests: Declaration of competing interest The authors declare no competing financial interests., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Electrochemical water oxidation utilizing bimetallic CoNi-Tz (Tz=1,2,4-triazole) framework is explored. Initially, CoNi-Tz possesses active tetrahedral Co center and electron-mediated octahedral Ni chain. After performing an electrochemical activation, the partial structural transformation on the Ni center occurs. This leads to the generation of excessive active centers which can promote catalytic activity of the framework. The activated CoNi-Tz catalyst displays a remarkably low OER overpotential of 293 mV at a current density of 10 mA cm -2 with a small Tafel slope of 49.98 mV dec -1 , outperforming the single metal Co-Tz and benchmark IrO 2 catalysts., (© 2024 Wiley-VCH GmbH.)

In recent years, there has been increasing attention towards understanding the relationship between age-related alterations in the oral microbiota and age-associated diseases, with reports emphasizing the significance of maintaining a balanced oral microbiota for host health. However, the precise mechanisms underlying age-related changes in the oral microbiota remain elusive. We recently reported that cellular senescence of ileal germinal center (GC) B cells, triggered by the persistent presence of commensal bacteria, results in diminished IgA production with aging and subsequent alterations in the gut microbiota. Consequently, we hypothesize that a similar phenomenon may occur in the oral cavity, potentially contributing to age-related changes in the oral microbiota. Examination of p16-luc mice, wherein the expression of the senescent cell marker p16 INK4a can be visualized, raised under specific pathogen-free (SPF) or germ-free (GF) conditions, indicated that, unlike ileal GC B cells, the accumulation of senescent cells in GC B cells of cervical lymph nodes increases with age regardless of the presence of commensal bacteria. Furthermore, longitudinal studies utilizing the same individual mice throughout their lifespan revealed concurrent age-related alterations in the composition of the oral microbiota and a decline in salivary IgA secretion. Further investigation involving Rag1 -/- mice transplanted with B cells from wild-type or p16 INK4a and p21 Waf1/Cip1 -double knockout mice unveiled that B cell senescence leads to reduced IgA secretion and alteration of the oral microbiota. These findings advance our understanding of the mechanism of age-associated changes in the oral microbiota and open up possibilities of their control., (© 2024 The Author(s). Aging Cell published by Anatomical Society and John Wiley & Sons Ltd.)

Cancer stem cells (CSCs), which are critical targets for cancer therapy as they are involved in drug resistance to anticancer drugs, and metastasis, are maintained by angiocrine factors produced by particular niches that form within tumor tissue. Secreted frizzled-related protein 1 (Sfrp1) is an extracellular protein that modulates Wnt signaling. However, the cells that produce Sfrp1 in the tumor environment and its function remain unclear. We aimed to elucidate angiocrine factors related to CSC maintenance, focusing on Sfrp1. Although Sfrp1 is a Wnt pathway-related factor, its impact on tumor tissues remains unknown. We investigated the localization of Sfrp1 in tumors and found that it is expressed in some tumor vessels. Analysis of mice lacking Sfrp1 showed that tumor growth was suppressed in Sfrp1-deficient tumor tissues. Flow cytometry analysis indicated that CSCs were maintained in the early tumor growth phase in the Sfrp1 knockout (KO) mouse model of tumor-bearing cancer. However, tumor growth was inhibited in the late tumor growth phase because of the inability to maintain CSCs. Real-time PCR results from tumors of Sfrp1 KO mice showed that the expression of Wnt signaling target genes significantly decreased in the late stage of tumor growth. This suggests that Sfrp1, an angiocrine factor produced by the tumor vascular niche, is involved in Wnt signaling-mediated mechanisms in tumor tissues., Competing Interests: Declarations. Conflict of interest: The authors declare no competing interests., (© 2024. The Author(s).)

Voltage-gated sodium (Na v ) channels govern membrane excitability by initiating and propagating action potentials. Consistent with their physiological significance, dysfunction, or mutations in these channels are associated with various channelopathies. Na v channels are thereby major targets for various clinical and investigational drugs. In addition, a large number of natural toxins, both small molecules and peptides, can bind to Na v channels and modulate their functions. Technological breakthrough in cryo-electron microscopy (cryo-EM) has enabled the determination of high-resolution structures of eukaryotic and eventually human Na v channels, alone or in complex with auxiliary subunits, toxins, and drugs. These studies have not only advanced our comprehension of channel architecture and working mechanisms but also afforded unprecedented clarity to the molecular basis for the binding and mechanism of action (MOA) of prototypical drugs and toxins. In this review, we will provide an overview of the recent advances in structural pharmacology of Na v channels, encompassing the structural map for ligand binding on Na v channels. These findings have established a vital groundwork for future drug development.

Despite numerous biomarkers being proposed for rheumatoid arthritis (RA), a gap remains in our understanding of their mechanisms of action. In this study, we discovered a novel role for gelsolin (GSN), an actin-binding protein whose levels are notably reduced in the plasma of RA patients. We elucidated that GSN is a key regulator of NLRP3 inflammasome activation in macrophages, providing a plausible explanation for the decreased secretion of GSN in RA patients. We found that GSN interacts with NLRP3 in LPS-primed macrophages, hence modulating the formation of the NLRP3 inflammasome complex. Reducing GSN expression significantly enhanced NLRP3 inflammasome activation. GSN impeded NLRP3 translocation to the mitochondria; it contributed to the maintenance of intracellular calcium equilibrium and mitochondrial stability. This maintenance is crucial for controlling the inflammatory response associated with RA. Furthermore, the exacerbation of arthritic symptoms in GSN-deficient mice indicates the potential of GSN as both a diagnostic biomarker and a therapeutic target. Moreover, not limited to RA models, GSN has demonstrated a protective function in diverse disease models associated with the NLRP3 inflammasome. Myeloid cell-specific GSN-knockout mice exhibited aggravated inflammatory responses in models of MSU-induced peritonitis, folic acid-induced acute tubular necrosis, and LPS-induced sepsis. These findings suggest novel therapeutic approaches that modulate GSN activity, offering promise for more effective management of RA and a broader spectrum of inflammatory conditions., Competing Interests: Competing interests: The authors declare no competing interests. Ethics approval: This study did not involve any human participants. Mouse studies were conducted in accordance with the protocols approved by the Department of Laboratory Animal Resources Ethical Committee of Yonsei University College of Medicine and the President of Nippon Medical School., (© 2024. The Author(s).)

Development of subtype-selective drugs for G protein-coupled receptors poses a significant challenge due to high similarity between subtypes, as exemplified by the three β-adrenergic receptors (βARs). The β 3 AR agonists show promise for treating the overactive bladder or preterm birth, but their potential is hindered by off-target activation of β 1 AR and β 2 AR. Interestingly, several β-blockers, which are antagonists of the β 1 ARs and β 2 ARs, have been reported to exhibit agonist activity at the β 3 AR. However, the molecular mechanism remains elusive. Understanding the underlying mechanism should facilitate the development of β 3 AR agonists with improved selectivity and reduced off-target effects. In this work, we determined the structures of human β 3 AR in complex with the endogenous agonist epinephrine or with a synthetic β 3 AR agonist carazolol, which is also a high-affinity β-blocker. Structure comparison, mutagenesis studies and molecular dynamics simulations revealed that the differences on the flexibility of D 3.32 directly contribute to carazolol's distinct activities as an antagonist for the β 2 AR and an agonist for the β 3 AR. The process is also indirectly influenced by the extracellular loops (ECL), especially ECL1. Taken together, these results provide key guidance for development of selective β 3 AR agonists, paving the way for new therapeutic opportunities., (© 2024 Wiley-VCH GmbH.)

Voltage-gated calcium (Ca v ) channels mediate Ca 2+ influx in response to membrane depolarization, playing critical roles in diverse physiological processes. Dysfunction or aberrant regulation of Ca v channels can lead to life-threatening consequences. Ca v -targeting drugs have been clinically used to treat cardiovascular and neuronal disorders for several decades. This review aims to provide an account of recent developments in the structural dissection of Ca v channels. High-resolution structures have significantly advanced our understanding of the working and disease mechanisms of Ca v channels, shed light on the molecular basis for their modulation, and elucidated the modes of actions (MOAs) of representative drugs and toxins. The progress in structural studies of Ca v channels lays the foundation for future drug discovery efforts targeting Ca v channelopathies.

Herein, a deep blue emitter (PI-TPB-CN) with a synergistic effect of hybridized local and charge transfer excited state (HLCT) and aggregation-induced emission (AIE) properties is successfully designed and synthesized to improve the performance of deep blue organic light-emitting diodes (OLEDs). It is constructed using a 1,2,4,5-tetraphenylbenzene (TPB) as an π-conjugated AIE core being asymmetrically functionalized with a phenanthro[9,10-d]imidazole (PI) as a weak donor (D) and a benzonitrile (CN) as an acceptor (A), thereby formulating D-π-A type fluorophore. Its HLCT and AIE properties verified by theoretical calculations, solvatochromic effects, and transient photoluminescence decay experiments, bring about a strong blue emission (452 nm) with a high photoluminescence quantum yield of 74 % in the thin film. PI-TPB-CN is successfully employed as a blue emitter in OLEDs. Non-doped OLED with the structure of ITO/HAT-CN (6 nm)/NPB (30 nm)/TCTA (10 nm)/PI-TPB-CN (30 nm)/TPBi (40 nm)/LiF (1 nm)/Al (100 nm) demonstrates excellent electroluminescence (EL) performance with blue emission (451 nm) and maximum external quantum efficiency (EQE max ) of 7.38 %. The device with a thinner layer of PI-TPB-CN (20 nm) and TPBi (30 nm) exhibits a deeper blue emission (444 nm) with CIE coordinates of (0.156, 0.096), a low turn-on voltage of 3.0 V, and EQE max of 6.45 %., (© 2024 Wiley-VCH GmbH.)

Background: Metabolic-dysfunction-associated steatotic liver disease (MASLD) is a progressive liver disorder that possesses metabolic dysfunction and shows steatohepatitis. Although the number of patients is globally increasing and many clinical studies have developed medicine for MASLD, most of the studies have failed due to low efficacy. One reason for this failure is the lack of appropriate animal disease models that reflect human MASLD to evaluate the potency of candidate drugs. Methods: We developed a novel choline-deficient and 0.11%-methionine-added high-fat diet (CDAHFD)-based (MASH) diet that can induce murine metabolic-dysfunction-associated steatohepatitis (MASH) without severe body weight loss. We performed kinetic analyses post-feeding and proposed an appropriate timing of MASH pathogenesis by quantitatively analyzing steatosis, inflammation, and fibrosis. Results: This MASH diet induced liver fibrosis earlier than the conventional CDAHFD model. In brief, lipid accumulation, inflammation, and fibrosis started after 1 week from feeding. Lipid accumulation increased until 8 weeks and declined thereafter; on the other hand, liver fibrosis showed continuous progression. Additionally, immune cells, especially myeloid cells, specifically accumulated and induced inflammation in the initiation stage of MASH. Conclusions: The novel MASH diet promotes the dynamics of lipid deposition and fibrosis in the liver, similar to human MASH pathophysiology. Furthermore, immune-cell-derived inflammation possibly contributes to the initiation of MASH pathogenesis. We propose this model can be the new pre-clinical MASH model to discover the drugs against human MASH by evaluating the interaction between parenchymal and non-parenchymal cells.

Understanding the mechanisms behind MYC-driven oncogenic transformation could pave the way for identifying novel drug targets. This study explored the role of CREPT in MYC-induced malignancy by generating MYC-transformed mouse embryonic fibroblasts (MEFs) with conditional CREPT deletion. Our results demonstrated that the loss of CREPT significantly impaired MYC-induced colony formation and cell proliferation, indicating that CREPT is essential for the malignant transformation of MEFs. Reintroducing CREPT in CREPT-deficient cells restored malignant properties. Furthermore, CREPT overexpression alone enhanced colony formation upon MYC induction but was insufficient to induce transformation without MYC, suggesting a cooperative interaction between CREPT and MYC in malignant transformation. CREPT deletion resulted in delayed cell cycle progression during the G2/M and S phases. CREPT enhanced the expression of MYC target genes by directly interacting with MYC through the CID domain of CREPT and the PEST domain of MYC. Arginine 34 of CREPT was identified as a critical residue for the interaction with MYC, and its mutation lost the ability of CREPT to promote MYC-driven colony formation and tumor growth in colorectal cancer models. Additionally, CREPT facilitated the recruitment of RNA Polymerase II to MYC-binding promoters, promoting transcriptional initiation of MYC-targeted genes. Our study also revealed a strong correlation between CREPT and MYC expression in various human cancers, particularly in colorectal cancer, where their interaction appears to play a significant role in tumorigenesis. These findings suggest that the CREPT-MYC interaction is crucial for the progression of MYC-driven cancers and presents a potential target for therapeutic intervention., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Repulsive Guidance Molecule A (RGMa) is well-recognized for its role in axon guidance. Recent studies have unveiled its diverse functions under pathological conditions within the central nervous system, such as spinal cord injury, multiple sclerosis, and Parkinson's disease. In this study, we explored the involvement of RGMa and the therapeutic effects of an anti-RGMa neutralizing antibody in a mouse model of vascular dementia (VaD). The VaD mouse model was established using the bilateral common carotid artery stenosis (BCAS) method. Immunohistochemical analysis revealed that these mice exhibited increased RGMa expression in the hippocampus, which coincided with reduced neurogenesis and impaired cholinergic innervation. These alterations manifested as cognitive impairments in the BCAS mice. Significantly, treatment with anti-RGMa neutralizing antibody reversed these pathological changes and cognitive deficits. Our findings suggest that RGMa plays a pivotal role in VaD pathology within the hippocampus and propose the anti-RGMa antibody as a promising therapeutic avenue for treating VaD., Competing Interests: Declaration of competing interest A humanized anti-RGMa monoclonal antibody (unasnemab/MT-3921) was developed by Osaka University, Chiba University, and Mitsubishi Tanabe Pharma Corporation and are the property of them. The Department of Neuro-Medical Science was co-founded by Osaka University and Mitsubishi Tanabe Pharma Corporation., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Through the decomposition of the pressure into the kinetic and the intermolecular contributions, we show that the pressure anisotropy in the fluid interface, which is the source of the interfacial tension, comes solely from the latter contribution. The pressure anisotropy due to the intermolecular force between the fluid particles in the same or the different fluid components is approximately proportional to the multiplication of the corresponding fluid density gradients, and from the molecular dynamics simulation of the liquid-vapor and liquid-liquid interfaces, we demonstrate that the density gradient theory by van der Waals gives the leading order approximation of the free energy density in inhomogeneous systems, neglecting the Tolman length., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).)

Cell-cell fusion is a vital biological process where the membranes of two or more cells merge to form a syncytium. This phenomenon is critical in various physiological and pathological contexts, including embryonic development, tissue repair, immune responses, and the progression of several diseases. Osteoclasts, which are cells from the monocyte/macrophage lineage responsible for bone resorption, have enhanced functionality due to cell fusion. Additionally, other multinucleated giant cells (MGCs) also arise from the fusion of monocytes and macrophages, typically during chronic inflammation and reactions to foreign materials such as prostheses or medical devices. Foreign body giant cells (FBGCs) and Langhans giant cells (LGCs) emerge only under pathological conditions and are involved in phagocytosis, antigen presentation, and the secretion of inflammatory mediators. This review provides a comprehensive overview of the mechanisms underlying the formation of multinucleated cells, with a particular emphasis on macrophages and osteoclasts. Elucidating the intracellular structures, signaling cascades, and fusion-mediating proteins involved in cell-cell fusion enhances our understanding of this fundamental biological process and helps identify potential therapeutic targets for disorders mediated by cell fusion., Competing Interests: Declarations. Ethics approval and consent to participate: The parabiosis experiment was approved by the Institutional Animal Experimental Committee of Osaka University. Consent for publication: Not applicable. Competing interests: The authors declare that they have no competing interests., (© 2024. The Author(s).)

Pattern recognition receptor (PRR)-mediated perception of damage-associated molecular patterns (DAMPs) triggers the first line of inducible defenses in both plants and animals. Compared with animals, plants are sessile and regularly encounter physical damage by biotic and abiotic factors. A longstanding problem concerns how plants achieve a balance between wound defense response and normal growth, avoiding overcommitment to catastrophic defense. Here, we report that two antagonistic systemin receptors, SYR1 and SYR2, of the wound peptide hormone systemin in tomato act in a ligand-concentration-dependent manner to regulate immune homeostasis. Whereas SYR1 acts as a high-affinity receptor to initiate systemin signaling, SYR2 functions as a low-affinity receptor to attenuate systemin signaling. The expression of systemin and SYR2, but not SYR1, is upregulated upon SYR1 activation. Our findings provide a mechanistic explanation for how plants appropriately respond to tissue damage based on PRR-mediated perception of DAMP concentrations and have implications for uncoupling defense-growth trade-offs., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

In the intestinal tract, where numerous intestinal bacteria reside, intestinal epithelial cells produce and release various antimicrobial molecules that form a complex barrier on the mucosal surface. These barrier molecules can be classified into two groups based on their functions: those that exhibit bactericidal activity through chemical reactions, such as antimicrobial peptides, and those that physically hinder bacterial invasion, like mucins, which lack bactericidal properties. In the small intestine, where Paneth cells specialize in producing antimicrobial peptides, the chemical barrier molecules primarily inhibit bacterial growth. In contrast, in the large intestine, where Paneth cells are absent, allowing bacterial growth, the primary defense mechanism is the physical barrier, mainly composed of mucus, which controls bacterial movement and prevents their invasion of intestinal tissues. The expression of these barrier molecules is regulated by metabolites produced by bacteria in the intestinal lumen and cytokines produced by immune cells in the lamina propria. This regulation establishes a defense mechanism that adapts to changes in the intestinal environment, such as alterations in gut microbial composition and the presence of pathogenic bacterial infections. Consequently, when the integrity of the gut mucosal barrier is compromised, commensal bacteria and pathogenic microorganisms from outside the body can invade intestinal tissues, leading to conditions such as intestinal inflammation, as observed in cases of inflammatory bowel disease., Competing Interests: Declarations. Conflict of interests: The authors declare no competing interests., (© 2024. The Author(s).)

Lithium solid-state batteries offer improved safety and energy density. However, the limited stability of solid electrolytes (SEs), as well as irreversible structural and chemical changes in the cathode active material, can result in inferior electrochemical performance, particularly during high-voltage cycling (>4.3 V vs Li/Li + ). Therefore, new materials and strategies are needed to stabilize the cathode/SE interface and preserve the cathode material structure during high-voltage cycling. Here, we introduce a thin (~5 nm) conformal coating of amorphous Nb 2 O 5 on single-crystal LiNi 0.5 Mn 0.3 Co 0.2 O 2 cathode particles using rotary-bed atomic layer deposition (ALD). Full cells with Li 4 Ti 5 O 12 anodes and Nb 2 O 5 -coated cathodes demonstrate a higher initial Coulombic efficiency of 91.6% ± 0.5% compared to 82.2% ± 0.3% for the uncoated samples, along with improved rate capability (10x higher accessible capacity at 2C rate) and remarkable capacity retention during extended cycling (99.4% after 500 cycles at 4.7 V vs Li/Li + ). These improvements are associated with reduced cell polarization and interfacial impedance for the coated samples. Post-cycling electron microscopy analysis reveals that the Nb 2 O 5 coating remains intact and prevents the formation of spinel and rock-salt phases, which eliminates intra-particle cracking of the single-crystal cathode material. These findings demonstrate a potential pathway towards stable and high-performance solid-state batteries during high-voltage operation., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Immune memory has long been considered a function specific to adaptive immune systems; however, adaptive immune memory alone has not fully explained the mechanism by which vaccines exert their protective effects against non-target pathogens. Recently, trained immunity, in which human monocytes vaccinated with bacillus Calmette-Guérin become highly responsive to pathogens other than Mycobacterium tuberculosis, has been reported. However, a phenomenon called endotoxin tolerance is also known, in which monocyte responsiveness is attenuated after the first lipopolysaccharide stimulation. These phenomena represent an altered innate immune response after the initial exposure to the stimulus, indicating that memories are formed in the innate immune system. In this review, we discuss trained immunity and endotoxin tolerance, known as innate immune memory, and innate immune memory formation by mRNA vaccines, which have been newly used in the COVID-19 pandemic and are considered important vaccine modalities in the future., (© 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.)

Experimental autoimmune encephalomyelitis (EAE) is the most widely used rodent model for multiple sclerosis. Interferon-γ (IFN-γ) and regulatory T cells (Tregs) are individually well known to play beneficial roles in amelioration of EAE. However, little is known about the relationship between IFN-γ and Tregs during the disease. Here, we show that IFN-γ polarizes Tregs into T helper 1 (Th1)-type Tregs (Th1-Tregs) to recover from EAE. Single-cell RNA sequencing analysis revealed that brain Tregs showed signs of IFN-γ stimulation during EAE. Loss of IFN-γ signaling in Tregs and of T cell-derived IFN-γ impaired the Th1-Treg polarization and worsened the disease. Moreover, selective ablation of Th1-Tregs using an intersectional genetic method promoted proinflammatory features of macrophages in the inflamed brains and exacerbated the EAE. Taken together, our study highlights a critical role of T cell-derived IFN-γ for Th1-Treg polarization in inflamed brain to ameliorate EAE., Competing Interests: Competing interests statement:The authors declare no competing interest.

Toxoplasma gondii (T. gondii) is a zoonotic protozoan parasite that causes congenital toxoplasmosis, including fetal death, abortion, stillbirth, morphological abnormalities, and premature birth. Primary T. gondii infection in pregnant women results in congenital toxoplasmosis. C-C chemokine receptor (CCR) 2 is reportedly a critical host defense factor against T. gondii infection. However, details of the role of CCR2 in the host immune response to T. gondii in congenital toxoplasmosis remain unclear. Here, we infected pregnant CCR2-deficient mice with T. gondii, resulting in stillbirth, embryonic resorption, fetal morphological abnormalities, and preterm delivery at significantly higher rates than those in pregnant wild-type (WT) mice. Consistent with the severity of abnormal pregnancy, a large area of placental hemorrhage and a large number of T. gondii infections around the hemorrhagic area were observed in the placentas of CCR2-deficient mice. In addition, the accumulation of inflammatory monocytes in the placenta was reduced in CCR2-deficient mice during infection. We further confirmed that the adoptive transfer of inflammatory monocytes collected from WT mice into T. gondii-infected pregnant CCR2-deficient mice effectively suppressed placental damage and abnormal pregnancy. Collectively, CCR2 contributes to pregnancy maintenance by regulating the migration of inflammatory monocytes into the placenta of T. gondii-infected pregnant mice., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Japanese Society for Immunology.)

The tumor microenvironment (TME) contains a number of immune-suppressive cells such as T helper 1-polarized regulatory T cells (T H 1-T reg cells). However, little is known about the mechanism behind the abundant presence of T H 1-T reg cells in the TME. We demonstrate that selective depletion of arginase I (Arg1)-expressing tumor-associated macrophages (Arg1 + TAMs) inhibits tumor growth and concurrently reduces the ratio of T H 1-T reg cells in the TME. Arg1 + TAMs secrete the chemokine platelet factor 4 (PF4), which reinforces interferon-γ (IFN-γ)-induced T reg cell polarization into T H 1-T reg cells in a manner dependent on CXCR3 and the IFN-γ receptor. Both genetic PF4 inactivation and PF4 neutralization hinder T H 1-T reg cell accumulation in the TME and reduce tumor growth. Collectively, our study highlights the importance of Arg1 + TAM-produced PF4 for high T H 1-T reg cell levels in the TME to suppress antitumor immunity.

An ideal codrug design should be able to control drug release, offer selectivity during drug delivery, and break down into non-toxic fragments after biodegradation. Our design incorporates d-ribofuranose as the core, with carbamate and carbonate groups as linking joints, a phosphodiester moiety as an enzyme recognition site, and lenalidomide and paclitaxel as the constituent drugs. The codrug synthesis involves seven steps with a 33% overall yield. The target codrug increases its water solubility 685 times versus paclitaxel.

Systemic lupus erythematosus (SLE) is an autoimmune disease, the pathophysiology and genetic basis of which are incompletely understood. Using a forward genetic screen in multiplex families with SLE, we identified an association between SLE and compound heterozygous deleterious variants in the non-receptor tyrosine kinases (NRTKs) ACK1 and BRK . Experimental blockade of ACK1 or BRK increased circulating autoantibodies in vivo in mice and exacerbated glomerular IgG deposits in an SLE mouse model. Mechanistically, NRTKs regulate activation, migration, and proliferation of immune cells. We found that the patients' ACK1 and BRK variants impair efferocytosis, the MERTK-mediated anti-inflammatory response to apoptotic cells, in human induced pluripotent stem cell (hiPSC)-derived macrophages, which may contribute to SLE pathogenesis. Overall, our data suggest that ACK1 and BRK deficiencies are associated with human SLE and impair efferocytosis in macrophages., Competing Interests: SG, TL, NJ, BB, MT, BC, TZ, CN, RB, HY, FR, RF, SD, DI, DD, NL, OE, AV, NS, LA, SN, MH, WM, JC, FG No competing interests declared, (© 2024, Guillet, Lazarov et al.)

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.)

Listeria monocytogenes causes listeriosis, a serious foodborne illness with a high mortality rate, especially in vulnerable populations. It accounts for 19% of foodborne deaths, with invasive cases having a mortality rate of up to 44%, leading to conditions like meningitis, bacteremia, and meningoencephalitis. However, the prognostic factors remain unclear. This study examines the hospital outcomes of invasive listeriosis and identifies risk factors for in-hospital and one-year mortality. We analyzed the electronic medical records of 118 hospitalized patients with non-perinatal, culture-proven invasive listeriosis collected over a 21-year period. The in-hospital mortality rate was 36.4%, with only 33.1% surviving one year and 22.0% surviving two years. The key findings indicate that a quick Sequential Organ Failure Assessment (qSOFA) score of ≥2 (OR 106.59, p < 0.001), respiratory failure (OR 7.58, p = 0.031), and shorter ampicillin duration (OR 0.53, p = 0.012) independently predicted poorer in-hospital outcomes. Additionally, a qSOFA score of ≥2 (OR 8.46, p < 0.001) and shorter ampicillin duration (OR 0.65, p < 0.001) were linked to higher one-year mortality. This study is the first to identify a qSOFA score of ≥2 as a significant marker for high-risk invasive listeriosis patients, with poorer outcomes linked to a qSOFA score of ≥2, respiratory failure, and shorter ampicillin use.

The cell fate of primordial germ cells (PGCs) in zebrafish is pre-determined by maternally deposited germ plasm, which is packaged into ribonucleoprotein complex in oocytes and inherited into PGCs-fated cells in embryos. However, the maternal factors regulating the assembly of germ plasm and PGC development remain poorly understood. In this study, we report that the maternal transcription factor Znf706 regulates the assembly of germ plasm factors into a granule-like structure localized perinuclearly in PGCs during migration. Maternal and zygotic mutants of znf706 (MZznf706) exhibit deficient germ plasm scattering at the early embryonic stage, decreased PGC numbers with some mislocation during PGC migration, and a lower female ratio in adulthood. Notably, the implementation of Znf706 CUT&Tag and RNA-seq on immature oocytes uncovers that Znf706 in stage I oocytes may promote transcription of several mitochondrial genes in addition to other functions. Hence, we propose that Znf706 is implicated in germ plasm assembly and PGC development in zebrafish., Competing Interests: Declaration of Competing Interest The authors announce no conflict of interest., (Copyright © 2024. Published by Elsevier Ltd.)

Novel van der Waals (vdW) contacts formed by layered Bi 2 Te 3 are found effective in improving the performance of WSe 2 pMOSFETs. As compared with conventional transition metal-based Ni/Au S/D contacts, over 10 3 times on-state current improvement is achieved. vdW interface formation between Bi 2 Te 3 and WSe 2 is confirmed by X-ray diffraction analysis and scanning transmission electron microscope observation. An atomically flat Bi 2 Te 3 /WSe 2 vdW interface, where the number of defects could be reduced as small as possible, contributes to the suppression of Fermi-level pinning caused by defect-induced gap states. Moreover, the semimetal-like characteristics of Bi 2 Te 3 are also effective in minimizing the impact of metal-induced gap states. These features offer WSe 2 pMOSFETs with exceptional S/D junction characteristics, including suppressed off-state leakage and a higher on-off ratio. In addition, it is found that WSe 2 pMOSFETs with Bi 2 Te 3 S/D contacts have excellent thermal stability, maintaining device performance even after 400 °C annealing, which is very promising for CMOS back-end-of-line application. The layered tellurides, reconciling low contact resistance and high thermal stability, are promising, particularly from the perspective of their application in the manufacturing process., Competing Interests: Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Genome-wide association studies (GWAS) statistically assess the association between tens of millions of genetic variants in the whole genome and a phenotype of interest. Genome-wide association studies enable the elucidation of polygenic inheritance of cancer, in which myriad low-penetrance genetic variants collectively contribute to a substantial proportion of the heritable susceptibility. In addition to the robust genotype-phenotype associations provided by GWAS, combining GWAS data with functional genomic datasets or sophisticated statistical genetic methods unlocks deeper insights. Integrating genotype and molecular phenotyping data facilitates functional characterization of GWAS association signals through molecular quantitative trait loci mapping and transcriptome-wide association studies. Furthermore, aggregating genome-wide polygenic signals, including subthreshold associations, enables one to estimate genetic correlations across diverse phenotypes and helps in clinical risk predictions by evaluating polygenic risk scores. In this review, we begin by summarizing the rationale for GWAS of cancer, introduce recent methodological updates in the GWAS-derived downstream analyses, and demonstrate their applications to GWAS of cancers., (© 2024 The Author(s). Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.)

Antibodies are powerful tools for the therapy and diagnosis of various diseases. In addition to conventional hybridoma-based screening, recombinant antibody-based screening has become a common choice; however, its application is hampered by two factors: (1) screening starts after Ig gene cloning and recombinant antibody production only, and (2) the antibody is composed of paired chains, heavy and light, commonly expressed by two independent expression vectors. Here, we introduce a method for the rapid screening of recombinant monoclonal antibodies by establishing a Golden Gate-based dual-expression vector and in-vivo expression of membrane-bound antibodies. Using this system, we demonstrate the rapid isolation of influenza cross-reactive antibodies with high affinity from immunized mice within 7 days. This system is particularly useful for isolating therapeutic or diagnostic antibodies, for example during foreseen pandemics., Competing Interests: TW, HH, YM, FY, TH, NK, TK, OO, HF No competing interests declared, (© 2024, Watanabe et al.)

Natural protein-protein communications, such as those between transcription factors (TFs) and RNA polymerases/ribosomes, underpin cell-free biosensing systems operating on the transcription/translation (TXTL) paradigm. However, their deployment in field analysis is hampered by the delayed response (hour-level) and the complex composition of in vitro TXTL systems. For this purpose, we present a de novo-designed ligand-responsive artificial protein-protein communication (LIRAC) by redefining the connection between TFs and non-interacting CRISPR/Cas enzymes. By rationally designing a chimeric DNA adaptor and precisely regulating its binding affinities to both proteins, LIRAC immediately transduces target-induced TF allostery into rapid CRISPR/Cas enzyme activation within a homogeneous system. Consequently, LIRAC obviates the need for RNA/protein biosynthesis inherent to conventional TXTL-based cell-free systems, substantially reducing reaction complexity and time (from hours to 10 minutes) with improved sensitivity and tunable dynamic range. Moreover, LIRAC exhibits excellent versatility and programmability for rapidly and sensitively detecting diverse contaminants, including antibiotics, heavy metal ions, and preservatives. It also enables the creation of a multi-protein communication-based tristate logic for the intelligent detection of multiple contaminants. Integrated with portable devices, LIRAC has been proven effective in the field analysis of environmental samples and personal care products, showcasing its potential for environmental and health monitoring., (© 2024 Wiley-VCH GmbH.)

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.)

Cord blood (CB)-derived chimeric antigen receptor (CAR)-natural killer (NK) cells targeting CD19 have been shown to be effective against B cell malignancies. While human CD56 + NK cells can be expanded in vitro , NK cells can also be differentiated from hematopoietic progenitor cells. It is still unclear whether CAR-NK cells originate from mature NK cells or NK progenitor cells in CB. Here, we determined that CAR-NK cells were predominantly derived from CD56 - NK progenitor cells. We first found that substantial numbers of CD19 CAR-NK cells were produced from CD56 - CB mononuclear cells after in vitro culture for 2 weeks. Single-cell RNA sequencing analysis of CD56 - CD3 - CD14 - CD19 - CB mononuclear cells revealed that these cells could be subdivided into three subpopulations based on the expression of CD34 and human leukocyte antigen (HLA)-DR. NK cells originated primarily from CD34 - HLA-DR - cells. In addition, among the CD34 - HLA-DR - cells, only CD7 + cells could differentiate into NK cells. These results indicate that CD56 - CD7 + CD34 - HLA-DR - lineage marker (Lin) - cells are the major origin of human CB-derived CAR-NK cells, indicating the importance of developing methods to enhance the quality and quantity of NK cells produced from these NK progenitor cells., Competing Interests: N.H. has applied for a Japanese patent entitled “NK progenitor cells and method of producing NK cells using the progenitor cells” through the Osaka University Office for University-Industry Collaboration., (© 2024 The Author(s).)

The tripartite ancestral structure is a recently proposed model for the genetic origin of modern Japanese, comprising indigenous Jomon hunter-gatherers and two additional continental ancestors from Northeast Asia and East Asia. To investigate the impact of the tripartite structure on genetic and phenotypic variation today, we conducted biobank-scale analyses by merging Biobank Japan (BBJ; n = 171,287) with ancient Japanese and Eurasian genomes (n = 22). We demonstrate the applicability of the tripartite model to Japanese populations throughout the archipelago, with an extremely strong correlation between Jomon ancestry and genomic variation among individuals. We also find that the genetic legacy of Jomon ancestry underlies an elevated body mass index (BMI). Genome-wide association analysis with rigorous adjustments for geographical and ancestral substructures identifies 132 variants that are informative for predicting individual Jomon ancestry. This prediction model is validated using independent Japanese cohorts (Nagahama cohort, n = 2993; the second cohort of BBJ, n = 72,695). We further confirm the phenotypic association between Jomon ancestry and BMI using East Asian individuals from UK Biobank (n = 2286). Our extensive analysis of ancient and modern genomes, involving over 250,000 participants, provides valuable insights into the genetic legacy of ancient hunter-gatherers in contemporary populations., Competing Interests: Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

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.)

The ongoing evolution and immune escape of SARS-CoV-2, alongside the potential threat of SARS-CoV-1 and other sarbecoviruses, underscore the urgent need for effective strategies against their infection and transmission. This study highlights the discovery of nanobodies from immunized alpacas, which demonstrate exceptionally broad and potent neutralizing capabilities against the recently emerged and more divergent SARS-CoV-2 Omicron subvariants including JD.1.1, JN.1, KP.3, KP.3.1.1, as well as SARS-CoV-1 and coronaviruses from bats and pangolins utilizing receptor ACE2. Among these, Tnb04-1 emerges as the most broad and potent, binding to a conserved hydrophobic pocket in the spike's receptor-binding domain, distinct from the ACE2 binding site. This interaction disrupts the formation of a proteinase K-resistant core, crucial for viral-cell fusion. Notably, intranasal administration of Tnb04-1 in Syrian hamsters effectively prevented respiratory infection and transmission of the authentic Omicron XBB.1.5 subvariant. Thus, Thb04-1 holds promise in combating respiratory acquisition and transmission of diverse sarbecoviruses., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Dong et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The rational manipulation of the surface reconstruction of catalysts is a key factor in achieving highly efficient water oxidation, but it is a challenge due to the complex reaction conditions. Herein, we introduce a novel in situ reconstruction strategy under a gradient magnetic field to form highly catalytically active species on the surface of ferromagnetic/paramagnetic CoFe 2 O 4 @CoBDC core-shell structure for electrochemical oxygen evolution reaction (OER). We demonstrate that the Kelvin force from the cores' local gradient magnetic field modulates the shells' surface reconstruction, leading to a higher proportion of Co 2+ as active sites. These Co sites with optimized electronic configuration exhibit more favorable adsorption energy for oxygen-containing intermediates and lower the activation energy of the overall catalytic reaction. As a result, a significant enhancement in OER performance is achieved with a large current density increment about 128 % at 1.63 V and an overpotential reduction by 28 mV at 10 mA cm -2 after reconstruction. Interestingly, after removing the external magnetic field, the activity could persist for over 100 h. This work showcases the directional surface reconstruction of catalysts under a gradient magnetic field for enhanced water oxidation., (© 2024 Wiley-VCH GmbH.)

Biomolecular condensates regulate transcription by dynamically compartmentalizing the transcription machinery. Classic models of transcription regulation focus on the recruitment and regulation of RNA polymerase II by the formation of complexes at the 1-10 nm length scale, which are driven by structured and stoichiometric interactions. These complexes are further organized into condensates at the 100-1,000 nm length scale, which are driven by dynamic multivalent interactions often involving domain-ligand pairs or intrinsically disordered regions. Regulation through condensate-mediated organization does not supersede the processes occurring at the 1-10 nm scale, but it provides regulatory mechanisms for promoting or preventing these processes in the crowded nuclear environment. Regulation of transcription by transcriptional condensates is involved in cell state transitions during animal and plant development, cell signalling and cellular responses to the environment. These condensate-mediated processes are dysregulated in developmental disorders, cancer and neurodegeneration. In this Review, we discuss the principles underlying the regulation of transcriptional condensates, their roles in physiology and their dysregulation in human diseases., (© 2024. Springer Nature Limited.)

Staphylococcus aureus can cause outbreaks and becomes multi-drug resistant through gene mutations and acquiring resistance genes. However, why S. aureus easily adapts to hospital environments, promoting resistance and recurrent infections, remains unknown. Here we show that a specific S. aureus lineage evolved from a clone that expresses the accessory gene regulator (Agr) system to subclones that reversibly suppressed Agr and caused an outbreak in the hospital setting. S. aureus with flexible Agr regulation shows increased ability to acquire antibiotic-resistant plasmids, escape host immunity, and colonize mice. Bacteria with flexible Agr regulation shows altered cytosine genomic methylation, including the decreased 5mC methylation in transcriptional regulator genes (pcrA and rpsD), compared to strains with normal Agr expression patterns. In this work, we discover how altered genomic methylation promotes flexible Agr regulation which is associated with persistent pathogen colonization in the hospital environment., (© 2024. The Author(s).)

A comprehensive endoscopic small and large intestinal untargeted step biopsy procedure was conducted to compare gene expression between the normal intestinal mucosa of healthy individuals and that of patients with colorectal tumors. From 78 participants (healthy individuals [n = 17], patients with colorectal conventional adenomas [n = 6], patients with Tis-T1 colorectal cancer [n = 41], patients with T2-4 colorectal cancer [n = 14]), biopsies of normal mucosa of the terminal ileum, right-sided colon (cecum and ascending colon), and left-sided colorectum (descending colon, sigmoid colon, and rectum) were obtained using a lower gastrointestinal endoscope. RNA was extracted from all samples, and total transcriptome sequencing was performed. Transcriptome data from 388 samples was analyzed. DNA was also extracted from tumor biopsy tissues and analyzed for whole-exome sequencing. In healthy individuals, gene expression differed significantly among the terminal ileum, right-sided colon, and left-sided colorectum, presumably linked to embryological factors. There were differences in gene expression in the normal mucosa in colorectal cancer patients, compared to healthy controls. Patients with tumors, especially T2-4 colorectal cancer, showed considerable variation in gene expression in non-tumor tissues, even in the terminal ileum distant from the tumor site. Based on endoscopic biopsies, the results imply cancer-predisposing conditions in seemingly normal tissues. The present study points to the importance of small intestine and cancer-predisposing conditions in the colon of colorectal cancer patients, with possible implications for developing novel immunotherapy and other therapeutic modalities., (© 2024. The Author(s).)

Wilms' tumor protein 1 (WT1)-targeted immunotherapy has been used in patients with leukemia and solid tumors. However, the spontaneous WT1-specific immune response before WT1 peptide vaccination in patients with WT1-expressing tumors (PTs) remains unclear. Therefore, we investigated whether WT1-specific cytotoxic CD8 + T-lymphocytes (CTLs) are clonally expanded in the peripheral blood outside of tumor sites. Clonal expansion of WT1 126 peptide (a.a.126-134)-specific CTLs (WT1 126 -CTLs) was compared between seven PTs and five healthy volunteers (HVs), and their T-cell receptors (TCRs) were analyzed at the single-cell level. Overall, 433 and 351 TCR β-chains of WT1 126 -CTLs were detected from PTs and HVs, respectively, and complementarity-determining region 3 was sequenced for clonality analysis. The frequencies of WT1 126 -CTLs were higher in human leukocyte antigen (HLA)-A*02:01 + PTs than in HLA-A*02:01 + HVs, although the difference was not statistically significant. WT1 126 -CTLs of differentiated types, including memory and effector, were higher in PTs than in HVs; whereas, those of the naïve type were higher in HVs than in PTs. WT1 126 -CTL clonality was significantly higher in PTs than in HVs. Furthermore, the frequency of effector WT1 126 -CTLs positively correlated with WT1 126 -CTL clonality in PTs; whereas, the frequency of naïve phenotype WT1 126 -CTLs tended to be negatively correlated with clonality. In conclusion, these results suggest that the WT1 protein in tumor cells is highly immunogenic, thereby stimulating endogenous naïve-type WT1 126 -CTLs and enabling them to clonally expand and differentiate into effector-type WT1 126 -CTLs., (© 2024. The Author(s).)

Predicting protein-small molecule binding sites, the initial step in structure-guided drug design, remains challenging for proteins lacking experimentally derived ligand-bound structures. Here, we propose CLAPE-SMB, which integrates a pre-trained protein language model with contrastive learning to provide high accuracy predictions of small molecule binding sites that can accommodate proteins without a published crystal structure. We trained and tested CLAPE-SMB on the SJC dataset, a non-redundant dataset based on sc-PDB, JOINED, and COACH420, and achieved an MCC of 0.529. We also compiled the UniProtSMB dataset, which merges sites from similar proteins based on raw data from UniProtKB database, and achieved an MCC of 0.699 on the test set. In addition, CLAPE-SMB achieved an MCC of 0.815 on our intrinsically disordered protein (IDP) dataset that contains 336 non-redundant sequences. Case studies of DAPK1, RebH, and Nep1 support the potential of this binding site prediction tool to aid in drug design. The code and datasets are freely available at https://github.com/JueWangTHU/CLAPE-SMB . SCIENTIFIC CONTRIBUTION: CLAPE-SMB combines a pre-trained protein language model with contrastive learning to accurately predict protein-small molecule binding sites, especially for proteins without experimental structures, such as IDPs. Trained across various datasets, this model shows strong adaptability, making it a valuable tool for advancing drug design and understanding protein-small molecule interactions., (© 2024. The Author(s).)

This single-center retrospective study aimed to analyze the variability of macrolide resistance (MR) in 68 patients with Mycobacterium avium complex pulmonary disease. Among 25 patients treated without macrolides, 13 (52%) reverted to macrolide-susceptible (MS) profiles. Only one (2%) of 43 patients who continued macrolide treatment showed this change. We compared 30 MR isolates with recent specimens. Among them, seven shifted to MS (five attributed to clonally related strains; two resulting from reinfection or polyclonal infection)., Competing Interests: The authors declare no conflict of interest.