Biology subjects

Ito, A.

Publications and source records attributed to Ito, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Metabolic outsourcing from ingested lactic acid bacteria extends Caenorhabditis elegans healthspan via bacterial amino acid and enzyme provision

Lactic acid bacteria promote longevity, yet the host-microbe metabolic mechanisms remain obscure. Using Caenorhabditis elegans, which lacks a urea cycle, we investigated how Lactococcus lactis JCM 5805 (Lc5805) extends lifespan. Live Lc5805 consumption upregulated 74 cuticle-formation genes, primarily collagens, supporting structural integrity for longevity without activating host stress responses. Multi-omics and UPLC-MS analyses revealed a dramatic accumulation of L-citrulline and L-ornithine, driven by high intestinal expression of bacterial arginine deiminase (arcA). The finding that heat-treated Lc5805 failed to induce citrulline accumulation and lifespan extension confirms that this metabolic outsourcing system, the operation of the arginine deiminase pathway, requires active metabolic and enzymatic activity by live bacteria in the gut. By utilizing bacterial metabolites and enzymes to fuel collagen maintenance, the host avoids endogenous energy expenditure. This study unveils a novel symbiotic paradigm of "Metabolic Outsourcing" governing organismal longevity.

physiology↗

bioRxiv2026

Initiating mammalian reproduction from a single male genome

Sex in mammals is unidirectionally determined by the configuration of sex chromosomes. In contrast, several species, including fishes, can switch sexes in response to environmental cues, illustrating the reproductive advantages of sexual plasticity. Thus, technologies that can bypass the unidirectional nature of mammalian sex determination could open new avenues in reproductive biology. Here, by establishing a method that enables robust Y-chromosome elimination in embryos, we provide a strategy to regulate sex in mice. We show that this approach efficiently induces male-to-female sex reversal by releasing the Y chromosome as micronuclei during early development. When integrated with optimized somatic cell nuclear transfer, it enabled the parallel production of both male and sex-reversed female mice from a single male genome source. Offspring were successfully obtained from crosses between these male and sex-reversed female clones, demonstrating that this "dual-sex cloning" strategy can initiate sexual reproduction solely from a male somatic genome. These findings highlight dual-sex cloning as a valuable platform for securing mammalian reproduction and biodiversity from limited genetic resources.

developmental biology↗

bioRxiv2026

The canine respiratory epithelium is a permissive ecosystem for influenza interspecies transmission and emergence

The outcome of virus spillover ranges from dead-end infections to pandemics and is underpinned by host-pathogen interactions as well as evolutionary and epidemiological processes. The emergence of novel influenza A viruses (IAVs) has been associated with reassortment events involving multiple species, highlighting the importance of reservoir and intermediate hosts in viral emergence. Highly pathogenic H5N1 IAVs of the 2.3.4.4b genotype have caused a panzootic affecting a broad range of mammals. The role of dogs--arguably the most popular companion animal and a natural host of IAVs--in the ecology of IAVs under this new zooepidemiological scenario is unknown. To address this, we characterised the glycome of the dog respiratory epithelium, infected canine tracheal explants with multiple IAVs (including canine H3N2 and H3N8, equine H3N8, avian H3N8 and H5N1, swine H1N1, human H1N1 and H3N2, and bovine H5N1 viruses), and determined their cellular tropism. We show that the respiratory tract of dogs presents abundant sialylated glycans known to act as IAV receptors. Further, most IAVs (including 2.3.4.4b viruses) infected and replicated in dog tracheas, targeting mainly ciliated cells. Serological testing showed evidence of influenza spillover infections in dogs from the UK. Overall, our results show that the canine respiratory tract can provide a suitable environment for the generation of new IAVs. Given the multi-host contact networks of dogs in nature, they could act as recipients, bridging hosts, and/or mixing vessels for multiple IAV lineages, playing a central role in the ecology of influenza emergence.

microbiology↗

bioRxiv2026

Identity-state expression and switching in co-conscious dissociative identity disorder: a non-traumatic proof-of-concept fMRI study

Dissociative identity disorder (DID) remains debated because identity-state phenomena are privately experienced and may be attributed to suggestion, simulation or role enactment. Most neuroimaging studies rely on symptom provocation or traumatic recall, which complicates interpretation and is poorly suited to co-conscious presentations where simultaneous awareness should make state differences hardest to detect. We applied Identity-State Characterization and Analysis (ID-SCAN), a non-traumatic, identity-cued functional magnetic resonance imaging protocol, to a DSM-5-diagnosed woman with persistent co-consciousness between Adult and Adolescent identity-states. One task used identical insect images that evoked opposite preferences across identity-states; the other used trait judgments about self, the other identity-state and a shared intimate other. Analyses combined Bayesian single-case general linear modelling, generalized psychophysiological interaction connectivity and searchlight representational similarity analysis. Identity-instruction cue epochs were pooled across tasks to assess switch direction. The same insect stimuli engaged different valuation-related configurations across identity-states: Adolescent-selective effects centred on striato-thalamic regions, whereas Adult-selective effects extended to amygdala and orbitofrontal/medial prefrontal cortex, with distinct task-evoked coupling. Adult-as-self and Adolescent-as-self occupied separable positions within canonical self-referential regions. Cue-locked activity differed by switch direction across tasks, with larger reconfiguration when switching to Adult (mean between-cluster beta separation 4.30 versus 0.85; permutation p = 0.0001). Cross-task overlap localized a limited shared task-related substrate mainly to posterior visual and dorsal parietal cortex. Even under persistent co-consciousness and without trauma provocation, identity-state expression and switching showed convergent within-person neural signatures. The findings support non-traumatic mechanistic phenotyping of dissociative presentations and motivate cohort and longitudinal studies, including treatment-tracking work.

neuroscience↗

bioRxiv2026

Tumor-infiltrating natural killer cell profiling for therapeutic stratification in patients with resectable non-small cell lung cancer

ObjectiveNeoadjuvant chemoimmunotherapy has improved outcomes in resectable non-small cell lung cancer (NSCLC), yet its real-world implementation is often challenged by surgical delays, immune-mediated fibrosis, and postoperative complications. Smokers with NSCLC, despite a high risk for surgical morbidity, show enhanced responses to neoadjuvant chemoimmunotherapy. This study aimed to identify smoking-associated immune cell determinants that could guide treatment strategies. MethodsSingle-cell RNA sequencing (scRNAseq) was performed on 61 lung tissues from non-smokers and smokers to identify smoking-related immune compositions. The scRNAseq data from 19 invasive lung adenocarcinomas were used to validate their presence in the tumor-immune microenvironment. Bulk RNA sequencing data from 102 resected NSCLC and 24 NSCLC patients treated with neoadjuvant chemoimmunotherapy followed by surgery were used for in silico cellular deconvolution and outcome analyses. ResultsAmong 135 lung cellular phenotypes, two natural killer (NK) cell subsets were strongly associated with smoking and chronic obstructive pulmonary disease (COPD) severity. "Stress-responsive" NK (NKSR) cells exhibited immature features and cytokine-responsive features, and "Adaptive and immunoregulatory NK" (NKAIR) cells showed mature features and elevated multiple immune checkpoint expression. High intratumoral NKSR cells correlated with improved survival after surgery, particularly in current smokers. Conversely, tumors with low NKSR and high NKAIR cells responded more favorably to neoadjuvant chemoimmunotherapy. ConclusionsIntratumoral NK cell phenotyping may aid in therapeutic stratification in patients with NSCLC. NKSR cell preservation predicts benefit from upfront surgery, while NKAIR cell enrichment indicates improved response to neoadjuvant chemoimmunotherapy. These NK cell profiles may help optimize treatment by balancing therapeutic benefit and risk. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/696292v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@168bc03org.highwire.dtl.DTLVardef@10fa947org.highwire.dtl.DTLVardef@132a92dorg.highwire.dtl.DTLVardef@100e4a4_HPS_FORMAT_FIGEXP M_FIG C_FIG Central Picture O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/696292v1_ufig2.gif" ALT="Figure 2"> View larger version (21K): org.highwire.dtl.DTLVardef@1a2d3b4org.highwire.dtl.DTLVardef@f8f84borg.highwire.dtl.DTLVardef@17510bcorg.highwire.dtl.DTLVardef@9da763_HPS_FORMAT_FIGEXP M_FIG C_FIG NK cell profiling for treatment stratification in resectable NSCLC Central MessageTumor-infiltrating NK cell profiling identifies distinct immune phenotypes that can inform personalized treatment strategies in resectable NSCLC. Perspective statementAbundance of intratumoral stress-responsive NK cells predicts favorable outcomes after upfront surgery, whereas enrichment of adaptive and immunoregulatory NK cells suggests greater benefit from neoadjuvant chemoimmunotherapy. These findings support incorporating NK-cell profiling into preoperative decision-making to optimize therapy selection and balance risks in the high-risk surgical population.

immunology↗

bioRxiv2025

HDA19-mediated deacetylation of histone H3.3 lysine 27 and 36 regulates plant sensitivity to salt stress

Plants survive extreme environments through rapid chromatin reprogramming, yet the epigenetic marks that confer stress resilience remain poorly understood. Histone deacetylase HDA19 is a key epigenetic regulator in Arabidopsis, and hda19-deficient mutants display tolerance to multiple abiotic stresses, including drought, heat, and salinity. Using lysine acetylome profiling, we identified a non-canonical K27/K36 di-acetylation mark on histone H3.3, among nine H3 variants, as a specific substrate of HDA19. Under salinity stress, this mark decreased in wild-type plants but increased in hda19 mutants, while other known H3 modifications were similarly affected in both genotypes. Mimicking constitutive di-acetylation of H3.3 K27/K36 through lysine-to-glutamine substitutions promoted accumulation of stress-responsive late embryogenesis abundant (LEA) proteins and conferred salinity tolerance in seedlings, phenocopying hda19 mutants. Furthermore, generating the lea7-1/lea29-1/rab18-1 triple mutant abolished hda19-dependent salinity tolerance, confirming the LEA proteins role downstream of HDA19. Our findings demonstrate that H3.3 K27/K36 di-acetylation, modulated by HDA19, drives LEA protein accumulation and enables plants to withstand environmental stress, revealing a previously unknown core mechanism of plant stress resilience. Significance statementHistone acetylation is crucial for regulating chromatin states and transcription, yet the specific histone codes controlled by histone deacetylases and acetyltransferases during plant stress acclimation remain unclear. Arabidopsis mutants lacking histone deacetylase 19 show enhanced tolerance to drought, heat, and salinity. Using acetylome profiling and genetic analyses, we identify a previously unknown di-acetylation of histone H3.3 at lysines 27 and 36 as a key epigenetic switch activating late embryogenesis abundant proteins essential for salt tolerance in seedlings. This discovery reveals a novel mechanism linking histone H3.3 K27/K36 di-acetylation to stress-resilient protein accumulation, offering new insights into epigenetic control of plant stress responses and informing strategies to improve crop resilience under climate change.

plant biology↗

bioRxiv2025

Diagnosing linearity along the carbon cascade in terrestrial biosphere models

Elevated carbon dioxide (eCO2) fertilises photosynthesis, driving an increase in terrestrial gross primary production (GPP). However, it is unclear how effectively increased GPP propagates along the "carbon (C) cascade" to increase net primary production (NPP) and vegetation C stocks (Cveg) in different plant compartments. Vegetation models simulate divergent C cycle projections and have been criticised for being overly photosynthesis-driven (source-driven), neglecting processes that lead to non-linear behaviour in response to the GPP increase, which may attenuate (or amplify) changes in NPP and vegetation C stocks. Here, we introduce an analytical framework to diagnose linearity (L) of the land C cycle as the ratio of relative changes in linked fluxes and pools and apply it to outputs from 16 models of the TRENDY v11 ensemble. We found widely varying patterns in L across models and for the different links. Six models showed a clear dominance of larger relative changes in NPP than in GPP in global simulations (LNPP:GPP >1 for >60% of gridcells), indicating increased carbon use efficiency under eCO2. Only three models had LNPP:GPP < 1 for >60% of gridcells. Four models showed a clear dominance of larger relative changes in steady-state Cveg than in NPP, while five models showed an opposite pattern - in both cases with a large spread of LCveg*:NPP across gridcells within models. Three models showed a larger relative increase in root C than in Cveg, while two models showed a clear dominance of the opposite pattern. Widely differing distributions of L across models and links reveal a strong influence of alternative process representations (nonlinear behaviour) in individual models. However, for all links, L deviations from 1 were roughly balanced across the model ensemble, leading to an overall linear behaviour of terrestrial C cycle representations.

ecology↗

bioRxiv2025

Psychological scales in the brain: Trait-linked questionnaire items evoke similar neural patterns in the mPFC

Self-report questionnaires are widely used across psychology and related disciplines, yet the cognitive and neural processes underlying how individuals generate responses to such items remain poorly understood. Here, we investigated whether items from the same psychological scale evoke similar neural activation patterns in the medial prefrontal cortex (mPFC), a region consistently implicated in self-referential processing. While undergoing functional magnetic resonance imaging (fMRI), participants completed a self-reference task in which they judged how well 72 personality-related questionnaire items (e.g., from the Big Five, emotion regulation, and well-being scales) described themselves. Using representational similarity analysis (RSA), we found that items from the same scale elicited more similar multivoxel activation patterns in the mPFC compared to items from different scales. This effect was specific to the self-reference task and was not observed during a semantic judgment control task using the same items. Furthermore, the mPFC encoded not only categorical scale membership but also graded psychological similarity among scales, as reflected in inter-scale behavioral correlations. Importantly, these effects remained significant even after controlling for sentence-level semantic similarity using multiple regression RSA, indicating that the observed neural structure reflects psychological rather than linguistic similarity. These findings suggest that the mPFC integrates internally constructed evidence in a construct-sensitive manner during self-report, and they open new avenues for linking psychological assessment with neural representation. We discuss the implications for understanding self-report as a cognitive process and for future work on neuroimaging-informed scale validation. Significance statementSelf-report questionnaires are widely used across psychology, medicine, and public policy to assess thoughts, feelings, and personality traits. However, little is known about how the brain generates these responses. Using fMRI and a multivariate analysis approach, we found that questionnaire items measuring the same psychological construct evoked similar activity patterns in the medial prefrontal cortex--a region involved in self-reflection. This effect was specific to self-referential judgments and remained significant even after controlling for sentence-level semantic similarity, suggesting that the brain organizes information according to underlying psychological traits rather than linguistic features. These findings offer new insights into how self-report operates at the neural level and may inform future approaches to scale development.

neuroscience↗

bioRxiv2025

Breast cancer identity is defined by specialized enhancer sets via lysine deacetylation

Breast cancer subtypes are defined by distinct transcriptional programs, yet the epigenetic mechanisms underlying subtype-specific gene regulation remain unclear. Enhancers, key regulators of gene expression and cell identity, are well positioned to define breast cancer subtypes. Here, we identify a previously unrecognized class of enhancers, termed hypoacetylation-defined (HD) enhancers, that regulate cancer-related genes in a luminal breast cancer cell line. HD enhancers are defined by RNA polymerase II dissociation upon lysine deacetylase inhibition, and bidirectional eRNA transcription. They are distinct from super-enhancers, require a specific Mediator subunit for gene-specific transcription, and form extensive chromatin interactions suggestive of a hub-like architecture. Analyses of clinical datasets further identified a subset of HD enhancers, termed HD cluster 1 enhancers, which classify patients into breast cancer subtypes and are associated with expression quantitative trait loci linked to subtype-specific gene expression. This study identifies the lysine deacetylation-regulated cell identity enhancers, which are potential therapeutic targets.

cancer biology↗

bioRxiv2025

Endothelial Sphingosine-1-Phosphate Receptor (S1PR) 1, a Functional S1PR in the Human Cerebrovascular Endothelium, Limits Blood Brain Barrier Permeability and Neuronal Injury following Subarachnoid Hemorrhage in Mice.

Hypoxia-induced blood-brain barrier (BBB) permeability has been identified as a key contributor to the progression of ischemic-hypoxic brain injury and neuronal dysfunction in stroke and other cerebrovascular diseases. Emerging clinical evidence highlights that the vasoprotective signaling properties of high-density lipoprotein (HDL), mediated through its bioactive lipid component sphingosine-1-phosphate (S1P), may be impaired in cardiovascular and inflammatory conditions. Nonetheless, the precise contributions and mechanistic roles of S1P signaling within the cerebral microvasculature remain insufficiently characterized. In this study, we aimed to elucidate the role of S1P signaling via its endothelial receptor S1PR1 in the pathophysiology of early brain injury following subarachnoid hemorrhage (SAH), a particularly severe form of stroke. Additionally, we sought to evaluate the relevance of the endothelial S1PR1 pathway in the human cerebrovascular endothelium, its functional role in hypoxia-induced cerebral endothelial barrier dysfunction, and its underlying molecular mechanisms. To address these objectives, we utilized endothelial-specific S1PR1 knockout mice subjected to the endovascular rupture model of aneurysmal SAH, performed mechanistic studies in primary human cerebral microvascular endothelial cells, and characterized S1PR1 expression in human brain tissue using validated protocols. Our findings reveal robust expression of S1PR1 in the cerebrovascular endothelium of both mice and humans. Functional analyses demonstrated that S1PR1 is critical for maintaining BBB integrity and mitigating neuronal injury in the context of SAH. Mechanistic in vitro studies indicated that S1PR1 exerts a vasoprotective effect by limiting hypoxia-induced BBB dysfunction in human primary brain microvascular endothelial cells through inhibition of Rho-associated kinase (ROCK)-mediated phosphorylation of myosin light chain (MLC), suppression of stress fiber formation and caveolin-1-dependent endosomal trafficking. These results highlight the pivotal role of endothelial S1PR1 signaling in preserving cerebral vascular integrity and provide a strong scientific foundation for developing novel therapeutic approaches targeting the S1P pathway in the endothelium to enhance neurovascular protection.

neuroscience↗

bioRxiv2024

Novel endornaviruses infecting Phytophthora cactorum that attenuate vegetative growth, promote sporangia formation, and confer hypervirulence to the host oomycete.

Two novel endornaviruses were found in Phytophthora cactorum isolated from severe black lesions on Boehmeria nivea (B. nivea) var. nipononivea plants in a Japanese forest. These two endornaviruses were named Phytophthora cactorum alphaendornavirus 4 (PcAEV4) and Phytophthora cactorum alphaendornavirus 5 (PcAEV5), and have site-specific nick structures in their positive RNA strands, which are hallmarks of alphaendornaviruses. Ribavirin and cycloheximide treatment of the protoplasts effectively cured the host oomycete (Kara1) of the viruses. The resultant virus-free strain (Kara1-C) displayed luxuriant mycelial growth with less zoosporangia formation as compared to the Kara1 strain. Remarkably, the Kara1-C strain exhibited reduced ability to form black lesions on B. nivea leaves, suggesting that presence of PcAEV4 and PcAEV5 in the Kara1 strain led to enhanced virulence in host plants. Under osmotic pressure and cell wall synthesis inhibition, the Kara1 strain exhibited less growth inhibition compared with the Kara1-C strain. In contrast, the Kara1 strain showed more growth inhibition to membrane-permeable surfactant compared with the Kara1-C strain, indicating that these endornaviruses can alter the susceptibility of the host oomycete to abiotic stresses. Co-localization and cell fractionation analyses showed that PcAEV4 and PcAEV5 localized to intracellular membranes, particularly the ER membrane fraction. Further, infection with these 2 endornaviruses was found to affect the hosts response to exogenous sterols, which enhanced vegetative growth and zoosporangia formation, as well as virulence of the host oomycete. These results provide deep insights into the effects of endornavirus infection in the Phytophthora spp. and also highlight protoplast-based methods in advancing Phytophthora virus studies.

microbiology↗

bioRxiv2024

SleepSatelightFTC: A Lightweight and Interpretable Deep Learning Model for Single-Channel EEG-Based Sleep Stage Classification

Sleep scoring by experts is necessary for diagnosing sleep disorders. To this end, electroen-cephalography (EEG) is an essential physiological examination. As manual sleep scoring based on EEG signals is time-consuming and labor-intensive, an automated method is highly desired. One promising automation technology is deep learning, which has performed well or better than experts in sleep scoring. However, deep learning lacks adequate interpretability, which is crucial for ensuring safety and accountability, especially for complex inference processes. We propose SleepSatelightFTC, a lightweight model that achieves comparable performance to state-of-the-art models with only one-third of their parameters. Based on the rules for sleep scoring, self-attention is applied to each of the time- and frequency-domain inputs, a raw EEG signal and its amplitude spectrum. The simple method of continuously connecting the intermediate outputs of the epoch-wise model has resulted in a highly lightweight architecture. On the Sleep-EDF-78 dataset, our model achieves an accuracy of 84.8% and a kappa coefficient of 0.787 while requiring significantly fewer parameters (0.47x 106) compared to existing models (1.3-4.54x 106). The visualization of feature importance obtained from self-attention confirms that the proposed model learns representative waveform features, including K-complexes and sleep spindles.

bioengineering↗

bioRxiv2024

Extracellular disposal of nuclear waste by APP: a protective mechanism impaired in Alzheimer's disease

Although the amyloid beta (A{beta}) hypothesis1 has long been central to Alzheimers disease (AD) research, effective therapeutic strategies remain elusive2,3. Here we re-evaluate the functions of amyloid precursor protein (APP) and reveal its critical function in protecting against nuclear impairment-induced cell death and inflammation4,5. Overexpression of APP mitigated etoposide or lamin A knockdown-induced nuclear damage, while APP removal or mutations exacerbated these effects. Interestingly, neurons differentiated from induced pluripotent stem cells (iPSCs) exhibited similar patterns, and notably, familial AD-associated mutant APP failed to confer protection against nuclear impairment. We identify APPs interaction with a cytoplasmic structure of nuclear origin, termed "nuclear waste", and propose its role in extracellular waste disposal. Intriguingly, cells lacking APP showed impaired nuclear waste clearance, leading to abnormal cytoplasmic accumulation of the nuclear waste. Similarly, neuron-specific APP overexpression using adeno-associated virus (AAV) in mice reduced neuronal death and inflammation caused by nuclear damage. Conversely, shRNA-mediated APP exacerbated these effects, and mutant APP associated with familial AD lacked protective effects. Moreover, postmortem analysis of AD brains revealed accumulation of abnormal nuclear waste in the neurocytoplasm, irregular nuclear morphology, and reduced APP levels per neuron. Our data underscore APPs crucial role in disposing of nuclear waste, maintaining cellular homeostasis, and suggest its dysregulation as a potential contributor to AD pathogenesis. Restoring APP waste clearance in AD could be a promising target for disease-modifying therapies.

neuroscience↗

bioRxiv2023

Chemical genetic interaction linking eIF5A hypusination and mitochondrial integrity

The eukaryotic translation factor eIF5A plays an important role in translation elongation, especially across stretches of prolines and charged amino acids, and in translation termination. eIF5A undergoes hypusination, a post-translational modification unique to this protein, although the role of hypusination in the function of eIF5A remains elusive. Here, we investigated the cellular defects induced by the hypusination inhibitor GC7 (N1-guanyl-1,7-diaminoheptane). Proteome, translatome, and transcriptome analyses indicated that GC7 downregulated a subset of mitochondrial proteins and DNA, causing mitochondrial stress and eliciting the integrated stress response. Chemical genomic screening using barcoded shRNA libraries identified genes encoding proteins involved in polyamine metabolism/transport and MPV17L2, a mitochondrial disease gene homologue whose product regulates mitochondrial translation. Depletion of MPV17L2 caused hypersensitivity to GC7 and phenocopied the effects of GC7 treatment. These results suggest that eIF5A hypusination and MPV17L2 synthetically regulate mitochondrial molecular synthesis and integrity.

cell biology↗

bioRxiv2023

Granulomatous inflammatory responses are elicited in the liver of PD-1 knockout mice by de novo genome mutagenesis

Aimsprogrammed death-1 (PD-1) is a negative regulator of immune responses. Upon deletion of PD-1 in mice, symptoms of autoimmunity developed only after they got old. In a model experiment in cancer immunotherapy, PD-1 was shown to prevent cytotoxic T lymphocytes from attacking cancer cells that expressed neoantigens derived from genome mutations. Furthermore, the larger number of genome mutations in cancer cells led to the more robust anti-tumor immune responses after the PD-1 blockade. In order to understand the common molecular mechanisms underlying these findings, we hypothesize that we might have acquired PD-1 during evolution in order to avoid/suppress autoimmune reactions against neoantigens derived from mutations in the genome of aged individuals. Main methods: to test the hypothesis, we introduced random mutations into the genome of young PD-1-/- and PD-1+/+ mice. We employed two different procedures of random mutagenesis: administration of a potent chemical mutagen N-ethyl-N-nitrosourea (ENU) into the peritoneal cavity of mice and deletion of MSH2, which is essential for the mismatch-repair activity in the nucleus and, therefore, for the suppression of accumulation of random mutations in the genome. Key findingswe observed granulomatous inflammatory changes in the liver of the ENU-treated PD-1 knockout (KO) mice, but not in the wild-type (WT) counterparts. Such lesions also developed in the PD-1/MSH2 double KO mice, but not in the MSH2 single KO mice. Significance: the results we obtained support our hypothesis: PD-1 probably functions to avoid/suppress inflammatory responses against neoantigens derived from genome mutations in aged individuals.

immunology↗

bioRxiv2022

Germinal center-derived broadly neutralizing antibodies adapt to SARS-CoV-2 antigenic drift

The outbreak of SARS-CoV-2 variant Omicron which harbors a striking number of mutations in the spike protein has been raising concerns about the effectiveness of vaccines and antibody treatment1. Here, we confirmed a substantial reduction in neutralizing potency against Omicron in all convalescent and vaccinated sera. However, we found that some people infected by the early strain show relatively higher neutralization to Omicron. From those B cells, we developed neutralizing antibodies inhibiting broad variants including Delta and Omicron. Unlike reported antibodies, one had an extremely large interface and widely covered receptor binding motif of spike, thereby interfering with diversified variants. Somatic mutations introduced by long-term germinal center reaction contributed to the key structure of antibodies and the universal interaction with spike variants. Recalling such rare B cells may confer sustainable protection against SARS-CoV-2 variants emerging one after another.

immunology↗

bioRxiv2022

Evaluation of heat inactivation of human norovirus in freshwater clams using human intestinal enteroids

Foodborne disease attributed to consumption of shellfish contaminated with human norovirus (HuNoV) is one of many global health concerns. Our study aimed to determine conditions of heat-inactivation of HuNoV in freshwater clams (Corbicula japonica) using a recently developed HuNoV cultivation system employing stem-cell derived human intestinal enteroids (HIEs). We first measured the internal temperature of clam tissue in a water bath during boiling at 90 {degrees}C and found that approximately 2 minutes are required for the tissue to reach 90 {degrees}C. Next, GII.4 HuNoV was spiked into the center of the clam tissue followed by boiling at 90 {degrees}C for 1, 2, 3, or 4 minutes. The infectivity of the HuNoV in clam tissue homogenates was evaluated using HIEs. We demonstrated that HuNoV in unboiled clam tissue homogenates replicated in HIEs, whereas infectivity was lost in all boiled samples, indicating that heat treatment at 90 {degrees}C for 1 minute is sufficient to inactivate HuNoV in freshwater clams. To our knowledge, this is the first study to determine the infectivity of HuNoV tolerability in shellfish using HIEs and our results will be informative to develop strategies to inactivate HuNoV in foods.

microbiology↗

bioRxiv2021

Role of TLR4 signaling on Porphyromonas gingivalis LPS-induced cardiac dysfunction in mice

Oral infections, particularly periodontitis, are a well-established risk factor for cardiovascular diseases, although the molecular mechanisms involved remain elusive. The aims of the present study were to investigate the effects of lipopolysaccharide derived from Porphyromonas gingivalis (PG-LPS) on cardiac function in mice, and to elucidate the underlying mechanisms. Mice (C57BL/6) were injected with PG-LPS (0.8 mg/kg/day) with or without an inhibitor of Toll-like receptor 4 (TLR4) signaling (TAK-242, 0.8 mg/kg/day) for 4 weeks. Left ventricular ejection function was significantly decreased at 1 week (from 67 {+/-} 0.5 to 58 {+/-} 1.2 %) and remained low at 4 weeks (57 {+/-} 1.0 %). The number of apoptotic myocytes was increased (approximately 7.4-fold), the area of fibrosis was increased (approximately 3.3-fold) and the number of 8-hydroxydeoxyguanosine-positive myocytes, a sensitive indicator of oxidative DNA damage, was increased (approximately 7.6-fold) at 4 weeks in the heart of PG-LPS treated mice. However, levels of various serum pro-inflammatory cytokines in PG-LPS-treated mice were similar to those in control mice. The impairment of cardiac function in PG-LPS-treated mice appears to involve activation of TLR4-NADPH oxidase (NOX) 4 signaling, leading to abundant production of reactive oxygen species and Ca2+ leakage from sarcoplastic reticulumn induced by calmodulin kinase II (CaMKII)-mediated phosphorylation of phospholamban (at Thr-17) and ryanodine receptor 2 (at Ser-2448). Pharmacological inhibition of TLR4 with TAK-242 attenuated the changes in cardiac function in PG-LPS-treated mice. Our results indicate that TLR4-NOX4 signaling may be a new therapeutic target for treatment of cardiovascular diseases in patients with periodontitis.

physiology↗