Biology subjects

Ota, A.

Publications and source records attributed to Ota, A..

13 recordsLinked to original sources

bioRxiv2026

A knockout screening platform for interferon-stimulated genes in respiratory cells identifies LY6E as a dominant antiviral effector against coronaviruses

Human coronaviruses (HCoVs) cause pathogenic outcomes ranging from mild illness to severe respiratory disease. Determining how respiratory cells coordinate an early antiviral response is necessary to understand successful control of HCoV replication. The Type I Interferon (IFN) response is a major component of innate viral immunity. IFN signaling leads to the upregulation of hundreds of interferon-stimulated genes (ISGs) that can have antiviral activity, though the individual ISGs that are responsible for restricting mildly pathogenic HCoVs in the respiratory epithelium are not clear. Here, we developed a targeted CRISPR-Cas9 knockout sgRNA library (termed the respISG library), focusing on ISGs that are upregulated across a panel of respiratory cells, to screen for innate host factors that restrict the mildly pathogenic human coronavirus, HCoV-OC43. We executed cell death-based screens in immortalized human small airway epithelial cells and identified lymphocyte antigen 6E (LY6E) as a top hit. We confirmed LY6E activity in validation studies and found it regulates entry of various SARS-CoV-2 Spike-pseudotyped lentiviruses. In addition to demonstrating a key role for LY6E in blocking a variety of HCoVs in small airway epithelial cells, this study establishes a loss-of-function CRISPR-Cas9 screening platform for identification of HCoV antiviral ISGs in respiratory cells.

microbiology↗

bioRxiv2026

West Nile virus capsid protein promotes viral replication and pathogenesis through PKCα-dependent lamin phosphorylation and nuclear deformation

The genus Orthoflavivirus comprises several medically important pathogens such as the West Nile virus (WNV), which causes encephalitis in humans. Although viral replication occurs in the cytoplasm, the capsid (C) protein of the orthoflavivirus is localized to both the cytoplasm and nucleus. Nuclear C protein contributes to viral replication and disease progression. However, the underlying mechanisms remain unclear. Here, we investigated whether the WNV C protein induces nuclear deformation and examined the underlying mechanism. We also assessed the contribution of this deformation to viral replication and pathogenesis. WNV infection and C protein expression induced morphological alterations in the nuclear lamina, leading to nuclear deformation. C protein expression enhanced lamin phosphorylation and the disassembly of the polymerized lamin network. In addition, C protein interacted with protein kinase C alpha (PKC) and localized PKC near the nuclear lamina. Downregulation of PKC expression inhibited C protein-induced lamin phosphorylation and nuclear deformation. In addition, both the downregulation of PKC expression and pharmacological inhibition of PKC reduced WNV replication. In contrast, the expression of phosphorylation-deficient lamin mutants attenuated the inhibitory effect of downregulated PKC expression on WNV replication. Furthermore, the pharmacological inhibition of PKC increased the survival rate of WNV-infected mice and suppressed both viral replication and nuclear deformation in the brain. Collectively, these results demonstrate that C protein remodels the nuclear lamina architecture through the PKC-lamin pathway, and that virus-induced nuclear deformation contributes to WNV replication and pathogenesis. Author summaryThe West Nile virus (WNV), a neurotropic orthoflavivirus, causes severe neurological diseases in humans. In host cells, orthoflaviviruses exclusively replicate in the cytoplasm. However, their capsid (C) proteins are localized to both the nucleus and cytoplasm. Although the nuclear C protein has been implicated in viral replication and disease progression, its underlying mechanisms remain unclear. Here, we demonstrate that the WNV C protein induces nuclear deformation, accompanied by the phosphorylation of lamin and disassembly of the nuclear lamina, a structural scaffold that maintains the nuclear shape. The C protein promotes the localization of PKC, a host kinase protein, near the nuclear lamina. Suppression of PKC expression or activity reduces lamin phosphorylation, nuclear deformation, and WNV replication. Importantly, pharmacological inhibition of PKC in WNV-infected mice reduced nuclear deformation and viral replication in the brain and improved survival rates. Collectively, our findings identify the host nucleus as an important site of WNV-host interaction and provide a new perspective that WNV, despite replicating in the cytoplasm, remodels host nuclear architecture to promote viral replication and pathogenesis.

microbiology↗

bioRxiv2026

EMPAC: A Multimodal Dataset for Bridging Affective and Cognitive Empathy

Empathy, a key element of social interaction, involves both cognitive and affective processes and is commonly investigated through measures such as empathic accuracy and affective physiological synchrony. While physiological synchrony offers a continuous measure of affective processes, empathic accuracy typically relies on discrete self-reports, leaving their temporal relationship largely unexplored. Advancing this line of research requires datasets that integrate time-continuous self-reports with physiological signals, yet such datasets--particularly those focusing on the empathizee--remain limited. To fill this gap, we present EMPAC (Empathy Measurement: Physiological, Affective, and Cognitive), a multimodal dataset constructed. To create empathy-eliciting stimuli, professional actors performed emotionally intense, pseudo-autobiographical narratives while their physiological signals (e.g., ECG, EDA) and continuous self-reported emotional states were recorded. We then conducted two observer experiments using these video recordings. In Experiment 1, to validate the stimuli as empathy-eliciting materials, observers continuously rated emotional intensity without being informed of the specific emotion portrayed, following the protocol of previous studies on time-series empathic accuracy. Yet this approach sometimes revealed a gap between the emotion category portrayed by the target and that perceived by the observers. In Experiment 2, we introduced a revised procedure in which the target emotion category was disclosed prior to viewing, revealing that specifying the target emotion led to a different relationship between individual empathy traits and empathic accuracy than observed in Experiment 1. EMPAC thus provides a rich, temporally aligned resource for investigating empathy dynamics in naturalistic settings and for evaluating methodological variations in empathic accuracy paradigms.

neuroscience↗

bioRxiv2026

scUnique: Measuring Ongoing Chromosomal Instability

Chromosomal instability is a hallmark of cancer that can drive tumour heterogeneity and treatment resistance. However, scalable methods to measure the dynamics of chromosomal instability are lacking and thus historic genomic scars can be hard to distinguish from markers of currently active mutational processes. Here, we introduce scUnique, a novel approach to measure ongoing chromosomal instability from single-cell whole genome sequencing (scWGS) data. scUnique performs phylogeny-aware joint segmentation to refine single-cell copy number profiles and identifies recent copy number aberrations as statistically supported changes on the leaves of the inferred phylogenetic tree. This yields a per-cell measure of ongoing chromosomal instability at genome-wide resolution. We validate scUnique in (i) a comprehensive benchmarking study, (ii) in CRISPR-Cas-based experimental systems, and (iii) single-cell derived clones of a well-characterised ovarian model. We show that scUnique distinguishes ongoing HRD and FBI mutational processes. These results show that scUnique provides quantitative, scalable, genome-level information about ongoing chromosomal instability, not available in previous studies relying on bulk DNA-sequencing or single-cell imaging. In the future, these improved measurements could refine the understanding of mechanisms of chromosomal instability and lead to dynamic biomarkers for improved treatment decisions.

cancer biology↗

bioRxiv2025

Early pathogenesis of spinal and bulbar muscular atrophy uncovered by human iPSC-derived motor neurons highlights pathogenic neuropeptides as therapeutic targets

Spinal and bulbar muscular atrophy (SBMA) is a neuromuscular disorder caused by the expansion of the polyglutamine tract in the androgen receptor (AR). Motor neurons (MNs) derived from patient-specific induced pluripotent stem cells (iPSCs) robustl y recapitulated early SBMA phenotypes driven by endogenous mutant AR in the absence of testosterone (dihydrotestosterone) and detectable mutant AR aggregation. Notably, endoplasmic reticulum stress markedly exacerbated SBMA pathology. Cross-species integrative analyses of patient-derived neurons and spinal cords of transgenic mouse models revealed high expression of multiple disease-associated neuropeptides, including urotensin II (UTS2), in patient spinal MNs that was correlated with disease onset and progression in iPSC-derived MNs. Downstream signaling analyses of these neuropeptides revealed convergent molecular pathways whose pharmacological inhibition rescued cellular phenotypes. Together, these results establish a human disease model harboring endogenous mutant AR that closely reproduces early SBMA pathology and provides molecular leads for elucidating disease mechanisms and biomarkers and developing therapeutic targets.

neuroscience↗

bioRxiv2022

A mouse model of insomnia with sleep apnea

Obstructive sleep apnea (OSA) patients are exposed to nighttime hypoxia during sleep by intermittent airway closure and feel daytime strong sleepiness. Strangely, insomnia co-occur in some OSA patients, which is called co-morbid insomnia and sleep apnea (COMISA). Here, we show activity responses to daytime hypoxia (DHx) in nocturnal mice were comparable to daytime sleepiness and co-occurring nighttime insomnia in COMISA. DHx reduced activity in active phase (AP) and increased following activity in activity ending phase (AEP). This down-and-up activity response (DUR) by DHx was also observed in molecular clock deficient Cry1 and Cry2 double knockout mice (CryDKO) expressing nighttime activity rise under light-dark cycle (LD) and not observed in arrhythmic CryDKO under constant darkness (DD). When daytime timing hypoxia was exposed at transition from LD to DD, about every 6 h down and up and down wavelike activity responses appeared in arrhythmic CryDKO. Results indicate this wavelike response and AP activity overlap and cause DUR in rhythmic mice. DHx increased plasma corticosterone and this increase antagonized AP activity reduction by DHx. DHx reduced forebrain adenosine and morning adenosine inhibition by caffeine induced DUR. Adenosine inhibition by caffeine or istradefylline at transition from LD to DD induced wavelike response in CryDKO. It is possible that wavelike response is damped oscillation because, interestingly, chronic caffeine treatment induced circasemidian and/or circadian activity rhythms in arrhythmic CryDKO. Evening caffeine attenuated DUR by DHx, which suggested adenosine inhibition chronotherapy may improve OSA/COMISA symptoms. Our animal model will be useful to understand COMISA. SignificanceObstructive sleep apnea patients (OSA) are exposed to nighttime hypoxia during sleep. OSA feels daytime strong sleepiness and increases risk of many diseases. Insomnia occurs in not a few OSA, which is called comorbid insomnia and sleep apnea (COMISA). We show here a mouse model of COMISA. In mice, daytime hypoxia exposure induced following down and up activity response (DUR), activity reduction in active phase and increase in activity ending phase, which corresponded to sleepiness and insomnia in COMISA. We found DUR was clock gene independent and might be driven by circasemidian system. Glucocorticoid and forebrain adenosine response were involved in DUR. Caffeine chronotherapy was effective in DUR. Our model may be useful to understand COMISA.

physiology↗

bioRxiv2022

LUZP1 regulates the constriction velocity of the contractile ring during cytokinesis

There has been a great deal of research on cell division and its mechanisms; however, its processes have not yet been entirely elucidated. To find novel proteins that regulate cell division, we performed the screening using siRNAs and/or the expression plasmid of the target genes and identified leucine zipper protein 1 (LUZP1). Recent studies have shown that LUZP1 interacts with various proteins and stabilizes the actin cytoskeleton; however, the function of LUZP1 in mitosis is not known. In this study, we found that LUZP1 colocalized with the chromosomal passenger complex (CPC) at the centromere in metaphase and at the central spindle in anaphase and that these LUZP1 localizations were regulated by CPC activity and kinesin family member 20A (KIF20A). Mass spectrometry analysis identified that LUZP1 interacted with death-associated protein kinase 3 (DAPK3), one regulator of the cleavage furrow ingression in cytokinesis. In addition, we found that LUZP1 also interacted with myosin light chain 9 (MYL9), a substrate of DAPK3, and comprehensively inhibited MYL9 phosphorylation by DAPK3. In line with a known role for MYL9 in the actin-myosin contraction, LUZP1 suppression accelerated the constriction velocity at the division plane in our timelapse analysis. Our study indicates that LUZP1 is a novel regulator for cytokinesis that regulates the constriction velocity of the contractile ring.

cell biology↗

bioRxiv2022

Unique genomic sequences in novel Mycobacterium avium subsp. hominissuis lineage enabled fine scale tracing the transmission route during pig movement

Mycobacterium avium subsp. hominissuis (MAH) is one of the most prevalent mycobacteria causing non-tuberculous mycobacterial disease in humans and animals. Of note, MAH is a major cause of mycobacterial granulomatous mesenteric lymphadenitis outbreaks in pig populations. To determine the precise source of infection of MAH in a pig farm and to clarify the epidemiological relationship among pig, human and environmental MAH lineages, we collected 50 MAH isolates from pigs reared in Japan and determined draft genome sequences of 30 isolates. A variable number of tandem repeat analysis revealed that most pig MAH isolates in Japan were closely related to North American, European and Russian human isolates but not to those from East Asian human and their residential environments. Historical recombination analysis revealed that most pig isolates could be classified into SC2/4 and SC3, which contain MAH isolated from pig, European human and environmental isolates. Half of the isolates in SC2/4 had many recombination events with MAH lineages isolated from humans in East Asia. To our surprise, four isolates belonged to a new lineage (SC5) in the global MAH population. Members of SC5 had few footprints of inter-lineage recombination in the genome, and carried 80 unique genes, most of which were located on lineage specific-genomic islands. Using unique genetic features, we were able to trace the putative transmission route via their host pigs. Together, we clarify the possibility of species-specificity of MAH in addition to local adaptation. Our results highlight two transmission routes of MAH, one exposure on pig farms from the environment and the other via pig movement. Moreover, our study also warns that the evolution of MAH in pigs is influenced by MAH from patients and their residential environments, even if the MAH are genetically distinct. HighlightsO_LIVariable number of tandem repeat analysis of Mycobacterium avium subsp. hominissuis (MAH) isolated from pigs (n=50) were conducted. C_LIO_LIDraft genome sequences of MAH (n=30) and genome analysis were conducted. C_LIO_LIPig MAHs were genetically far from East Asian human isolates and close to those of Western countries. C_LIO_LINovel MAH lineage which were transmitted farms by pig movement was found. C_LIO_LIHuman MAH isolates influenced the evolution of pig isolates. C_LI

microbiology↗

bioRxiv2021

Genome-wide association study reveals putative bacterial risk factors for cavitary Mycobacterium avium complex lung disease

Mycobacterium avium complex (MAC) lung disease is a slowly progressive disease, and its increasing incidence has garnered increased research interests. Cavitary MAC lung disease is associated with a higher mortality rate. Though genetic studies have unraveled the human risk factors, the role of microbial factors on pathogenesis behind the disease remains elusive. In this study, M. avium isolates were collected from sputum specimens of 109 distinct Japanese patients with or without a cavity (60 with a cavity and 49 without cavity) in a hospital located in Osaka prefecture. M. avium genomes were sequenced and searched for DNA motifs associated with cavity formation using a bacterial GWAS. Excluding known macrolide resistance mutations; cavity formation was found to be primarily associated with variants of cytochrome P450 of the CYP139 family, type I polyketide synthase Pks13, and the promoter region of an operon encoding membrane-anchored protease FtsH and folate synthesis pathway enzymes. Cavity risk variants at these three loci were frequent in the MahEastAsia2 lineage among the six lineages detected in M. avium global populations. Furthermore, the study demonstrated a correlation between the cavity risk promoter variant and increased sulfamethoxazole/trimethoprim resistance. Together, these findings suggest that natural variation in the biosynthesis and maintenance processes of M. avium membrane components influences the disease type of MAC lung disease. Although further validation is needed, the bacterial genetic markers listed in the present study could contribute to prognosis prediction based on bacterial genotyping and help develop treatment strategies in the future. IMPORTANCENontuberculous mycobacterial lung disease is of great concern in countries with an increasingly aging population. The disease types can largely be classified into non-cavitary nodular bronchiectasis and cavitary diseases (fibrocavitary, nodular bronchiectasis with cavity) that require different treatment strategies depending on the causal agents. Several studies have reported human risk factors for the disease; however, little efforts were made to investigate the risk factors in nontuberculous mycobacteria. Moreover, molecular genetics experiments have been difficult to search for virulence factors in M. avium, which the population genomics approaches could overcome. Here, the GWAS results suggested variants in three chromosomal loci associated with mycobacterial membrane components as risk factors for cavitary MAC lung disease. These findings could help develop treatment strategies for MAC lung disease in the future.

microbiology↗

bioRxiv2021

Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan.

Mycobacterium avium subsp. hominissuis (MAH) is one of the most important agents causing non-tuberculosis mycobacterial infection in humans and pigs. Genome analysis on MAH of human isolates has been proceeding, however, those of pigs are limited despite its potential source of infection to human. In the current study, we obtained 30 draft genome sequences of MAH of pigs reared in Japan. The 30 draft genomes consisted of 4,848,678 - 5,620,788 bp length, 4,652 - 5,388 coding genes and 46 - 75 (Med: 47) tRNAs. All isolates had restriction modification associated genes and 185 - 222 predicted virulence genes. Two isolates had tRNA arrays and one isolate had a clustered regularly interspaced short palindromic repeat (CRISPR) region. Our results will be useful for evaluation of the ecology of MAH by providing a foundation for genome-based epidemiological studies.

microbiology↗

bioRxiv2020

Diversification of the restriction modification system of Streptococcus pyogenes through its acquisition of mobile elements

Restriction-modification (RM) systems are typically regarded as "primitive immune systems" in bacteria. The roles of methylation in gene regulation, segregation, and mismatch repair are increasingly recognized. To analyze methyltransferase (MTase) diversity in Streptococcus pyogenes, we compared the RM system distribution in eight new complete genome sequences obtained here and in the database-deposited complete genome sequences of 51 strains. The MTase gene distribution showed that type I MTases often change DNA sequence specificity via switching target recognition domains between strains. The type II MTases in the included strains fell into two groups: a prophage-dominant one and a CRISPR-dominant one. Some highly variable type II MTases were found in the prophage region, suggesting that MTases acquired from phage DNA can generate methylome diversity. Additionally, to investigate the possible contribution of DNA methylation to phenotype, we compared the methylomes and transcriptomes from the four most closely related strains, the results of which suggest that phage-derived methylases possibly regulate the methylome, and, hence, regulate expression levels in S. pyogenes. Our findings will benefit further experimental work on the relationship between virulence genes and pathogenicity in S. pyogenes.

microbiology↗

bioRxiv2020

Area-specific Biased Global Efficiency in Functional Connectivity Provides Features Negatively Correlated with Age

It has been acknowledged that graph-theoretical coefficients computed from the adjacency matrix of cerebral resting-state functional connectivity (RSFC) represent aging of the brain and its plasticity facilitating cognitive reserve. In particular, global efficiency (GE) has been recognized as a crucial graph index for age-dependent RSFC. Using the dataset of the Nathan Kline Institute-Rockland Sample [NKI-RS], we found that the regions of the brain in which GE values decay with age were located in the subcortical zone and the cerebellum, whereas an opposite relationship was found in many frontal and parietal regions. Based on this systematic tendency, a new coefficient was proposed that corrects GE, referred to as biased GE (BGE); BGE is calculated by changing the sign of the weight between the superior and the inferior parts of the brain before separately averaging the respective sign groups of area-specific corrected GE values, to influence the raw global network GE. The BGE showed a significant negative correlation with age, irrespective of the scan condition, and strong consistency as an information source of a subjects identity. We propose that this new index could play an important role in the clinical context of preventive medicine and the maintenance of healthy brains.

neuroscience↗

bioRxiv2019

Tandem paired nicking promotes precise genome editing with scarce interference by p53

Targeted knock-in mediated by double-stranded DNA cleavage is accompanied by unwanted insertions and deletions (indels) at on-target and off-target sites. A nick-mediated approach scarcely generates indels but exhibits reduced efficiency of targeted knock-in. Here, we demonstrate that tandem paired nicking, a method for targeted knock-in involving two Cas9 nickases that create nicks at the homologous regions of the donor DNA and the genome in the same strand, scarcely creates indels at the edited genomic loci, while permitting the efficiency of targeted knock-in largely equivalent to that of the Cas9 nuclease-based approach. Tandem paired nicking seems to accomplish targeted knock-in via DNA recombination analogous to Hollidays model, and creates intended genetic changes in the genome without introducing additional nucleotide changes such as silent mutations. Targeted knock-in through tandem paired nicking neither triggers significant p53 activation nor occurs preferentially in p53-suppressed cells. These properties of tandem paired nicking demonstrate its utility in precision genome engineering.

molecular biology↗