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Ikeda, Y.

Publications and source records attributed to Ikeda, Y..

At least 19 recordsLinked to original sources

Two closely related RNA helicases, UAP56 and URH49, couple mRNA splicing and export pathways with their distinct complexes

Transcription and mRNA processing are integrated into appropriate mRNA export pathway(s) enabling fine-tuned gene expression. The closely related RNA helicases, UAP56 and URH49, form distinct complexes known as the apo-TREX and the apo-AREX complexes, respectively, which remodel into the ATP-TREX complexes, thus forming multiple mRNA export pathways. However, the mechanisms by which helicases and their complexes shape these pathways remain unclear. Here, we showed that UAP56 and URH49 play general roles in mRNA splicing ahead of export. Further analyses revealed three patterns of splicing regulation and their association with mRNA export: Type I, in which both helicases redundantly or synergistically regulate splicing within the same transcripts, associated with cooperative mRNA export; Type II, in which either helicase preferentially regulates splicing in distinct transcripts; and Type III, in which the helicases exert opposing splicing effects within the same transcripts. Type II and III regulation was associated with selective mRNA export. Moreover, we demonstrated that the distinct complex formation influenced the splicing patterns regulated by the two helicases. Our findings reveal an additional layer of transcriptome regulation mediated by UAP56, URH49, and their complexes, extending beyond their canonical roles in mRNA export.

molecular biology↗

Genome-wide evidence for cryptic multi-generational introgression between invasive Bursaphelenchus xylophilus and native B. mucronatus

Hybridization between invasive and native species can generate novel genetic variation with ecological and evolutionary consequences, yet introgression often remains cryptic. We investigated natural hybridization between the invasive pinewood nematode Bursaphelenchus xylophilus, the causal agent of pine wilt disease, and native Bursaphelenchus mucronatus in Japan. Using multiplexed inter-simple sequence repeat genotyping by sequencing, we genotyped 342 field-collected nematodes and then conducted pedigree-calibrated analysis using HIest v2.0, based on 48 highly informative diagnostic single-nucleotide polymorphisms (SNPs), followed by ADMIXTURE, complementary NeighborNet and principal component analyses of a broader 2,756-SNP dataset. The results identified nine high-confidence hybrids (2.6%) across two consecutive years (2023-2024), including relatively balanced F1-like individuals and strongly parentally biased advanced backcross-like individuals, demonstrating recurrent, multigenerational introgression. Four hybrids (44.4%) were undetectable using a single-locus diagnostic marker, showing that advanced introgression can escape conventional surveillance. Chemotaxis assays detected no volatile-mediated pre-mating discrimination, whereas post-mating barriers were incomplete and asymmetric. Crosses with B. xylophilus as the maternal parent showed reduced hatchability, particularly with B. mucronatus mucronatus, while reciprocal crosses generally retained higher hatchability, although some showed reduced fecundity. These results provide a mechanistic basis for natural gene flow in a recent secondary contact zone. Because B. mucronatus kolymensis is widespread in Europe and produces viable hybrid offspring with B. xylophilus in both directions, pathogen establishment could create new opportunities for introgression. Our findings reveal cryptic, multigenerational introgression between an invasive forest pathogen and its native congener, highlighting the importance of genomic surveillance for forest disease management and invasion-risk assessment under climate change.

evolutionary biology↗

Zuranolone mitigates delirium-like bispectral EEG changes, behavioral deficits, and neuroinflammation across surgical and inflammatory mouse models and age groups

Delirium is an acute, fluctuating brain dysfunction that commonly follows surgery and systemic inflammation, disproportionately affects older adults, and remains difficult to quantify continuously over time and treat pharmacologically. Here, we tested whether the neuroactive steroid zuranolone, a positive allosteric modulator of synaptic and extrasynaptic GABA_A receptors, mitigates delirium-like abnormalities across two complementary murine delirium models, a lipopolysaccharide-induced systemic inflammation (LPS) model and a postoperative delirium (POD) model, primarily in young and aged mice, with selected analyses in super-aged mice. Using continuous EEG with a validated bispectral EEG (BSEEG) metric, we found that zuranolone attenuated delirium-like EEG slowing in the LPS model in young mice in a dose-dependent manner and retained efficacy in aged mice. In the POD model, prophylactic dosing provided limited benefit in young mice, whereas post-surgery treatment reduced postoperative BSEEG elevations. In aged mice, prophylactic dosing suppressed POD-associated BSEEG abnormalities, and in super-aged mice, prophylactic zuranolone improved survival after POD induction. In parallel, zuranolone reduced microglial density and activation markers (IBA1 and CD68 immunoreactivity) at 24 h after POD surgery and after LPS challenge, with effects that were particularly evident in peri-screw site tissue in young POD mice and more broadly distributed across regions in aged mice. Finally, in young mice, zuranolone improved a composite behavioral severity score in the LPS model, whereas behavioral effects in the POD model were modest and domain-specific. Together, these findings support zuranolone as a candidate strategy to reduce delirium-like electrophysiological and neuroimmune abnormalities, with the strongest effects in inflammation-driven and age-vulnerable contexts.

neuroscience↗

Integrating spatial and single-cell multi-omics analysis of induced pluripotent stem cell-derived cervical adenocarcinoma model

Human papillomavirus 18 (HPV18) preferentially infects cervical stem cell-like cells and is strongly associated with adenocarcinoma. However, the mechanisms underlying differentiation into cervical adenocarcinoma remain unclear due to the lack of appropriate experimental models. We aimed to establish a model of HPV18-associated cervical adenocarcinoma and elucidate its molecular and cellular differentiation mechanisms. HPV18 E6/E7 were introduced into induced pluripotent stem cell-derived reserve cell-like cells (iRCs) to generate tumor models. Spatial transcriptomics and single-cell multi-omics analyses were performed to integrate histological and molecular data. A distinct component (Gland_A) exhibited morphological and immunohistochemical features of cervical adenocarcinoma and was efficiently induced in iRC-18 tumors. Gland_A showed increased chromatin accessibility and elevated expression of FOXA1, FOXA2, and ALDH1A1. Analysis of clinical samples confirmed enrichment of ALDH1A1 in HPV-associated adenocarcinomas. This model recapitulates key features of HPV18-associated cervical adenocarcinoma and provides insights into its differentiation mechanisms.

cancer biology↗

DECREASE IN DNA METHYLATION 1-mediated epigenetic regulation maintains gene expression balance required for heterosis in Arabidopsis thaliana

Heterosis, or hybrid vigor, is characterized by superior phenotypic performance in F hybrids compared to their parental lines, and its expression is influenced by both genetic and epigenetic factors. In this study, we investigated the role of epigenetic regulation, particularly DNA methylation mediated by DECREASE IN DNA METHYLATION 1 (DDM1), in early seedling biomass heterosis using hybrids between Arabidopsis thaliana accessions Columbia-0 and C24. Loss of DDM1 function in F hybrids resulted in a significant reduction of rosette diameter, confirming that DDM1 is essential for heterosis. Transcriptomic and epigenomic analyses revealed extensive genotype-specific changes in gene expression and DNA methylation patterns in ddm1 mutants. Notably, ddm1-F hybrids exhibited upregulation of genes categorized into xyloglucan:xyloglucosyl transferase activity and downregulation of genes categorized into circadian rhythm, which may contribute to reduced growth vigor. Whole-genome bisulfite sequencing showed widespread hypomethylation in ddm1 mutants, yet the overlap between differentially methylated and expressed genes was limited, suggesting indirect or context-dependent regulatory effects. Additionally, we examined the role of salicylic acid (SA) in heterosis using SA-deficient mutants and found that variations in endogenous SA levels did not correlate with biomass heterosis under normal conditions. Our findings suggest that heterosis in A. thaliana is dependent on the maintenance of parental epigenetic divergence, particularly in DNA methylation patterns mediated by DDM1. Disruption of DDM1 compromises this epigenetic complementarity, leading to transcriptomic imbalances that reduce heterosis. HighlightLoss of DDM1 reduces biomass heterosis in Arabidopsis thaliana hybrids by disrupting DNA methylation and transcriptome stability, revealing a novel salicylic acid-independent epigenetic mechanism.

plant biology↗

Highly selective SGLT2 inhibitors suppress glucose uptake in alpha-TC1 cells, while glucagon secretion is not affected.

The existence of sodium-glucose cotransporter 2 (SGLT2) in pancreatic alpha cells and its potential roles in glucagon secretion remain controversial, despite its well-established function in renal glucose reabsorption. While some studies suggest SGLT2 presence and its involvement in glucagon regulation, others deny its expression in alpha cells. To clarify this dispute, we investigated the functional effects of highly selective SGLT2 inhibitors, dapagliflozin and empagliflozin, on glucose uptake, intracellular ATP levels, and glucagon secretion in alpha-TC1 cells, a widely used model for glucagon-secreting cells in culture. The SGLT2 inhibitors significantly suppressed basal glucose uptake in alpha-TC1 cells, indicating functional SGLT2 presence. However, the inhibitors did not affect glucagon secretion. Neither the SGLT2 inhibitors nor the more potent glucose transport inhibitor, cytochalasin B, altered intracellular ATP levels or glucagon secretion. In contrast, pharmacological inhibition of K/ATP channels increased glucagon secretion without affecting glucose uptake or ATP levels. These results suggest that while SGLT2 is functionally present at low levels and mediates basal glucose uptake in alpha-TC1 cells, its inhibition has insufficient influence on intracellular ATP levels, and therefore glucagon secretion remains stable. Furthermore, our observations support predominant involvement of K/ATP channels in regulating glucagon secretion. Further studies in human purified pancreatic alpha cells in addition to islets are warranted to fully elucidate SGLT2s role in alpha-cell physiology.

pharmacology and toxicology↗

Tumor-microvessel on-a-chip reveals sequential intravasation cascade of cancer cell clusters

Circulating tumor cell (CTC) clusters are often detected in blood samples of patients with high-grade tumor and are associated with tumor metastasis and poor prognosis. However, the underlying mechanisms by which CTC clusters are released from primary tumors beyond blood vessel barriers remain unclear. In this study, a three-dimensional (3D) in vitro culture system is developed to visualize tumor intravasation by positioning tumor organoids with distinct genetic backgrounds to surround microvessels. We visualized tumor intravasation in a cluster unit, including collective migration in the collagen gel, vessel co-option, and the release of CTC clusters as one of cluster invasion manners yet reported previously. In addition, our results show that both transforming growth factor-{beta} (TGF-{beta}) expression in tumor cells and subsequent induction of activin expression in endothelium are essential for tumor cell intravasation accompanied with endothelial-to-mesenchymal transition (EndoMT) in microvessels. Our 3D in vitro system can be used to develop therapeutic strategies for tumor metastasis by targeting CTC clusters.

cancer biology↗

Spatiotemporal observation reveals metastatic tumor-driven vascular remodeling as a potential route to polyclonal colonization

Polyclonal metastasis, which arises from clusters of circulating tumor cells, promotes metastasis development and has become a major target of metastasis inhibition. Mouse experiments have clearly verified that nonmetastatic and metastatic tumors coexist and form metastatic nests, but the detailed mechanism of extravasation remains unclear. We established a three-dimensional tumor microvessel model to investigate extravasation between nonmetastatic tumors, metastatic tumors, and mosaic tumor organoids in a mixed state by time-lapse imaging and to determine the sequential steps of the extravasation of tumor cells via vascular remodeling. This comparison revealed a new concept of extravascular invasion via vascular remodeling in metastatic carcinoma. Furthermore, the involvement of liver host cells, the hepatic stellate cells, demonstrated an interaction with metastatic cells to facilitate metastatic foci formation. Moreover, Adam28 was highly expressed exclusively in metastatic tumor cells, suggesting its involvement in vascular remodeling. These results demonstrate the ability of metastatic tumor cells for extravasation in polyclonal metastasis, which may lead to the development of new therapeutic targets.

cancer biology↗

Rapid and dynamic evolution of a giant Y chromosome in Silene latifolia

To test hypotheses about the evolution of massive sex-linked regions in plants, we sequenced the genome of Silene latifolia, whose giant heteromorphic sex chromosomes were first discovered in 1923. It has long been known that the Y consists mainly of a male-specific region which does not recombine with the X in male meiosis, and that this region carries the primary sex-determining genes, and other genes contributing to male functioning. However, only with a whole Y chromosome assembly can the candidates be validated experimentally, as we describe. Our new results also illuminate the genomic changes as the ancestral chromosome evolved into the current XY pair, testing ideas about why large regions of sex-linkage evolve, and the mechanisms creating the present recombination pattern. One sentence summaryBased on the whole genome sequences of Silene latifolia, a model species for plant sex chromosome evolution, we describe discovery of genes underlying male-female flower differences, and relate the results to ideas about the evolution of the vast non-recombining regions of the Y chromosome.

genetics↗

Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by single-cell transcriptomics

Oxidative phosphorylation defects results in mitochondrial diseases, with cardiac involvement markedly impacting prognosis. However, the mechanisms underlying the transition from compensation to dysfunction in response to metabolic deficiency remain unclear, impeding the development of effective treatments. Here, we employed single-nucleus RNA sequencing (snRNA-seq) on hearts from mitochondrial cardiomyopathy (MCM) mice with cardiac-specific Ndufs6 knockdown (FS6KD). Pseudotime trajectory analysis of cardiomyocytes from early stage of female FS6KD hearts revealed dynamic cellular state transitioning from compensation to severe compromise, coincided with transient upregulation of a critical transcription factor, activating transcription factor 3 (Atf3). Genetic ablation or adeno-associated virus-mediated Atf3 knockdown in FS6KD mice effectively delayed cardiomyopathy progression in a female-specific manner. Notably, human MCM snRNA-seq revealed a similar transition, including the dynamic expression of ATF3. In conclusion, our findings highlight a fate-determining role of Atf3 in female MCM progression, providing a promising therapeutic candidate for the currently intractable disease.

cell biology↗

Universal method for generating knockout mice in multiple genetic backgrounds using zygote electroporation

Genetically engineered mouse models are essential tools for understanding mammalian gene functions and disease pathogenesis. Genome editing allows for the generation of these models in multiple inbred strains of mice without backcrossing. Zygote electroporation dramatically removed the barrier for introducing the CRISPR-Cas9 complex in terms of cost and labour. However, the editing conditions and protocols to produce knockout lines have been optimised for a limited number of strains or stocks. Here, we demonstrate a novel and universal approach for generating knockout mice in multiple inbred strains. By combining in vitro fertilisation and electroporation, we obtained founders for knockout alleles in 8 common inbred strains. Long-read sequencing analysis detected not only intended mutant alleles but also differences in read frequency of intended and unintended alleles among strains. Successful germline transmission of knockout alleles demonstrated that our novel approach can establish mutant mice targeting the same locus in multiple inbred strains for phenotyping analysis, contributing to reverse genetics and human disease research. Summary statementUniversal method for zygote genome editing in multiple inbred mouse strains allows for generation of novel mutant mice for understanding mammalian gene function and human disease pathogenesis.

genetics↗

Kaempferol suppresses the activation of mast cells by modulating the expression of FcϵRI and SHIP1

In the present study, we evaluated the effects of kaempferol on bone marrow-derived mast cells (BMMCs). Kaempferol treatment significantly and dose-dependently inhibited IgE-induced degranulation, and cytokine production of BMMCs under the condition that cell viability was maintained. Kaempferol downregulated the surface expression levels of Fc{varepsilon}RI on BMMCs, but the mRNA levels of Fc{varepsilon}RI, {beta}, and {gamma}-chains were not changed by kaempferol treatment. Furthermore, the kaempferol-mediated downregulation of surface Fc{varepsilon}RI on BMMCs was still observed in the presence of a protein-synthesis inhibitor. These results suggest that kaempferol reduced the surface Fc{varepsilon}RI on BMMCs, independently of transcription and translation. We also found that kaempferol inhibited both LPS- and IL-33-induced IL-6 production from BMMCs, without affecting the expression levels of their receptors, TLR4 and ST2. Although kaempferol treatment increased the protein amount of NRF2, a master transcription factor of antioxidant stress, in BMMCs, inhibition of NRF2 did not alter the suppressive effect of kaempferol on degranulation. Finally, we observed that kaempferol treatment increased the levels of mRNA and protein of a phosphatase SHIP1 in BMMCs. These results indicate that kaempferol inhibited the IgE-induced activation of BMMCs by downregulating Fc{varepsilon}RI and upregulating SHIP1, and the SHIP1 increase is involved in the suppression of various signaling-mediated stimulations of BMMCs, such as those associated with TLR4 and ST2.

immunology↗

Immunostimulatory effects of Bacillus coagulans SANK70258

Specific intestinal bacteria modulate immunoresponses through various pathways, and several probiotic bacteria have been identified as immunostimulants by screening. In the present study, we evaluated the immunomodulating effects of Bacillus coagulans SANK70258 (B. coagulans SANK70258), a spore-forming and lactic acid-producing bacterium usable as food supplement for human and animals. We found that treatment of mouse splenocytes with {gamma}-ray irradiated B. coagulans SANK70258 induced high amount of IFN-{gamma} in comparison with 7 kinds of typical lactic acid bacteria. Further analyses using splenocytes revealed that NK cell is a major source of IFN-{gamma}, and B. coagulans SANK70258-induced IFN-{gamma} production was inhibited by neutralization of IL-12 or IL-23, depletion of CD11c+ cells, and inhibition of NF{kappa}B. B. coagulans SANK70258 also induced release of IFN-{gamma} from activated CD8+ T cells, and increased expression of chemokine receptors in CD8+ T cells. B. coagulans SANK70258-treatment induced production of cytokines from bone marrow-derived dendritic cells, which is reduced by knockdown of Tlr2 and Nod2. B. coagulans SANK70258-treatment also induced IgA production from Peyers patch cells with high level among tested lactic bacteria. The oral intake of {gamma}-ray irradiated B. coagulans SANK70258 significantly increased intestinal IgA levels and IgA-expressing B cells in the Peyers patch of mice. Taken together, we conclude that B. coagulans SANK70258 possesses high activity as immunostimulant inducing production of IFN-{gamma} and IgA.

immunology↗

Decoy Receptor Fine-tunes Cytokinin Signaling

Hormone perception and signaling pathways play a fundamental regulatory function in cell growth, developmental, and physiological processes in both plant and animal systems. Those pathways are activated by hormone binding to the receptor to trigger cellular responses. Equally important are mechanisms that suppress activated transduction cascades to reset the system. Different mechanisms at the level of hormone biosynthesis and deactivation through degradation, conjugation, and production of repressors that attenuate transduction cascades downstream of receptors are known. In animal systems, decoy receptors have been identified as another important mechanism for fine-tuning the activity of the signaling pathways in processes like inflammatory responses, apoptosis, and blood vessel formation. Decoy receptors recognize and bind specific signaling molecules, but they cannot activate downstream signaling pathways thus providing competitive inhibition. Here we describe the first decoy receptor in plants. We show that the splicing variant of CRE1/AHK4 receptor of cytokinin, a hormone with a key role in the regulation of cell division and meristem maintenance in plants, acts as a decoy receptor to attenuate cytokinin signaling. We propose that this novel mechanism of signaling control applies in processes when modulation of CK signaling is needed.

plant biology↗

FGF21 protects against hepatic lipotoxicity and macrophage activation to attenuate fibrogenesis in nonalcoholic steatohepatitis

Analogues of the hepatokine FGF21 are in clinical development for type 2 diabetes and nonalcoholic steatohepatitis (NASH) treatment. Although their glucose-lowering and insulin-sensitizing effects have been largely unraveled, the mechanisms by which they alleviate liver injury have only been scarcely addressed. Here, we aimed to unveil the mechanisms underlying the protective effects of FGF21 on NASH using APOE*3-Leiden.CETP mice, a well-established model for human-like metabolic diseases. Liver-specific FGF21 overexpression was achieved in mice, followed by administration of a high-fat high-cholesterol diet for 23 weeks. FGF21 prevented hepatic lipotoxicity, accompanied by activation of thermogenic tissues and attenuation of adipose tissue inflammation, improvement of hyperglycemia and hypertriglyceridemia, and upregulation of hepatic programs involved in fatty acid oxidation and cholesterol removal. Furthermore, FGF21 inhibited hepatic inflammation, as evidenced by reduced Kupffer cell (KC) activation, diminished monocyte infiltration and lowered accumulation of monocyte-derived macrophages. Moreover, FGF21 decreased lipid- and scar-associated macrophages, which correlated with less hepatic fibrosis as demonstrated by reduced collagen accumulation. Collectively, hepatic FGF21 overexpression limits hepatic lipotoxicity, inflammation and fibrogenesis. Mechanistically, FGF21 blocks hepatic lipid influx and accumulation through combined endocrine and autocrine signaling, respectively, which prevents KC activation and lowers the presence of lipid- and scar-associated macrophages to inhibit fibrogenesis.

pathology↗

Highly efficient protein expression of Plasmodium vivax surface antigen, Pvs25 by silkworm, Bombyx mori, and its biochemical analysis.

Plasmodium vivax ookinete surface protein, Pvs25 is a transmission-blocking vaccine (TBV) candidate for malaria. Pvs25 has four EGF-like domains containing 22 cysteine residues forming 11 intramolecular disulfide bonds and this structural feature makes recombinant expression of Pvs25 difficult. In this study, we report the high expression of recombinant Pvs25 as a soluble form in silkworm, Bombyx mori. The Pvs25 protein was purified from hemolymphs of larvae and pupae by affinity chromatography. In the Pvs25 expressed by silkworm, no isoform with inappropriate disulfide bonds was found, requiring no further purification step which is necessary in case of Pichia pastoris based expressions systems. The Pvs25 from silkworm were confirmed to be the molecularly uniform by sodium dodecyl sulfate gel electrophoresis analysis and size exclusion chromatography analysis. To examine the immunogenicity, the Pvs25 from B. mori, was administered to BALB/c mice by the subcutaneous (s.c.) route with the oil adjuvant. The Pvs25 produced by silkworm induced potent and robust immune response, and the induced antisera correctly recognized P. vivax ookinetes in vitro, demonstrating the potency of Pvs25 from silkworm as a TBV candidate for malaria. This is the first study that to construct a mass production system for malaria TBV antigens by the silkworm to the best of our knowledge.

biochemistry↗

Fractal scaling of C. elegans behavior is shaped by insulin signaling

Fractal scaling governs the complex behavior of various animal species and, in humans, can be altered by neurodegenerative diseases and aging1. However, the mechanism underlying fractal scaling remains unknown. Here, we videorecorded C. elegans that had been cultured in a microfluidic device for 3 days and analyzed temporal patterns of C. elegans actions by fractal analyses. The residence-time distribution of C. elegans shared a common feature with those of human and mice2-4. Specifically, the residence-time power-law distribution of the active state changed to an exponential-like decline at a longer time scale, whereas this change did not occur in the inactive state. The exponential-like decline disappeared in starved C. elegans but was restored by culturing animals with glucose. The exponential-like decline similarly disappeared in insulin-signaling daf-2 and daf-16 mutants. Therefore, we conclude that insulin signaling regulates fractal scaling of C. elegans behavior. Our findings indicate that neurosensory modulation of C. elegans behavior by insulin signaling is achieved by regulation of fractal scaling. In humans, diabetes mellitus is associated with depression, bipolar disorder, and anxiety disorder5, which affect daily behavioral activities. We hypothesize that comorbid behavioral defects in patients with diabetes may be attributed to altered fractal scaling of human behavior.

animal behavior and cognition↗

CCG*CGG interruptions in high penetrance SCA8 families increase RAN translation and protein toxicity

Spinocerebellar ataxia type 8 (SCA8), a dominantly inherited neurodegenerative disorder caused by a CTG*CAG expansion, is unusual because most individuals that carry the mutation do not develop ataxia. To understand the variable penetrance of SCA8 we studied the molecular differences between highly penetrant families and more common sporadic cases (82%) using a large cohort of SCA8 families (N=77). We show that repeat expansion mutations from individuals with two or more affected family members have CCG*CGG interruptions at a higher frequency than sporadic SCA8 cases and that the number of CCG*CGG interruptions correlates with age at onset. At the molecular level, CCG*CGG interruptions increase RNA hairpin stability and steady state levels of SCA8 RAN polyAla and polySer proteins. Additionally, the CCG*CGG interruptions, which encode arginine interruptions in the polyGln frame increase the toxicity of the resulting proteins. In summary, CCG*CGG interruptions increase polyAla and polySer RAN protein levels, polyGln protein toxicity and disease penetrance and provide novel insight into the molecular differences between SCA8 families with high vs. low disease penetrance.

genetics↗