Biology subjects

Kumagai, Y.

Publications and source records attributed to Kumagai, Y..

9 recordsLinked to original sources

bioRxiv2025

Gelsolin Counteracts ER Stress-Driven Inflammatory Circuits in Psoriasis-like Dermatitis

Psoriasis is a chronic inflammatory skin disorder driven by amplified communication between immune cells and keratinocytes. Here, we show that imiquimod (IMQ) triggers organelle stress responses that directly contribute to this pathogenic circuit. In dendritic cells (DCs), IMQ promotes formation of ER-mitochondria contact sites (MAMs), inducing ER stress and activation of the unfolded protein response (UPR). These pathways act independently of, yet converge with, TLR7/MyD88 signaling to enhance IL-23 expression. IMQ also increases cytosolic Ca{superscript 2}+, facilitating NLRP3 inflammasome activation and release of mitochondrial DNA (mtDNA). In parallel, keratinocytes exposed to IMQ activate UPR-dependent genes, including Defb14 (mBD14), a psoriasis-associated antimicrobial peptide. Extracellular mtDNA and mBD14 then cooperatively stimulate plasmacytoid DCs through TLR9, establishing a feed-forward inflammatory loop. We further identify Gelsolin as a direct IMQ-binding protein that mitigates IMQ-induced ER stress; its loss amplifies ER stress, UPR activation, and oxidative stress, and its expression is reduced in human psoriatic lesions. Thus, MAM-UPR signaling links intracellular organelle stress to the intercellular networks that drive psoriatic inflammation, with Gelsolin acting as a critical intrinsic safeguard.

immunology↗

bioRxiv2025

Flow-driven construction of capillary-scale vessels with predefined geometries in natural hydrogels

Forming capillary networks with predefined geometries is a critical challenge in engineering complex three-dimensional tissues in vitro. While bioprinting and microfluidic technologies have enabled vascular tissue fabrication, precise control over capillary-scale vascularization remains limited. In this study, we investigated vascular formation process along hydrogel microchannels to elucidate mechanisms governing capillary-scale lumen formation. Microchannels were fabricated by femtosecond laser ablation in collagen and fibrin hydrogels. We optimized multiphoton lithography parameters to fabricate microchannels within these hydrogels and analyzed vascular formation along the channels. Luminal vascular structures formed readily in 50-m channels, while vascular formation failed in 20-m channels under static conditions, suggesting a significant shift in endothelial organization at the cellular scale. Flow stimulation significantly promoted vessel formation through collective endothelial cell migration and adhesion, whereas static conditions induced endothelial-to-mesenchymal transition. These findings provide key insights into capillary-scale vascularization and contribute to the development of more complex architectures with predefined shapes.

bioengineering↗

bioRxiv2025

Canonical Wnt/β-catenin signalling regulates inducible aging and regeneration loss in hydra

Freshwater cnidarians from the genus Hydra have exceptional regeneration capacities and show negligible aging. However, one species, Hydra oligactis, experiences accelerated senescence following sexual reproduction, characterized by regeneration loss, stem cell depletion, reduced body size, motility and food capture rates. This phenomenon, termed inducible aging, is triggered by temperature-induced sexual reproduction. The physiological regulation of the switch from high regenerative capacity and low senescence to regeneration loss and accelerated aging remain largely unexplored. By comparing gene expression patterns of asexual and sexual polyps following amputation we identified several canonical Wnt/{beta}-catenin signalling pathway transcripts that showed differential expression in the regeneration-deficient sexual individuals, suggesting the involvement of this pathway in the inducible aging phenotype. Pharmacological activation of canonical Wnt/{beta}-catenin signalling with alsterpaullone (ALP) restored head regeneration and improved survival of animals. To find out more about the role of this pathway in sexual development and post-reproductive senescence, we treated animals in various stages of egg maturation with ALP. We found that ALP delayed egg maturation when applied in early stages, but had smaller effects when applied in later stages of gametogenesis, without having a stark effect on overall fecundity. ALP treatment increased survival following sexual reproduction. These results show that the canonical Wnt/{beta}-catenin signalling pathway regulates reproduction, regeneration and post-reproductive senescence in H. oligactis.

developmental biology↗

bioRxiv2024

BootCellNet, a resampling-based procedure, promotes unsupervised identification of cell populations via robust inference of gene regulatory networks.

Recent advances in measurement technologies, particularly single-cell RNA sequencing (scRNA-seq), have revolutionized our ability to acquire large amounts of omics-level data on cellular states. As measurement techniques evolve, there has been an increasing need for data analysis methodologies, especially those focused on cell-type identification and inference of gene regulatory networks (GRNs). We have developed a new method named BootCellNet, which employs smoothing and resampling to infer GRNs. Using the inferred GRNs, BootCellNet further infers the minimum dominating set (MDS), a set of genes that determines the dynamics of the entire network. We have demonstrated that BootCellNet robustly infers GRNs and their MDSs from scRNA-seq data and facilitates unsupervised identification of cell clusters using scRNA-seq datasets of peripheral blood mononuclear cells and hematopoiesis. It has also identified COVID-19 patient-specific cells and their potential regulatory transcription factors. BootCellNet not only identifies cell types in an unsupervised and explainable way but also provides insights into the characteristics of identified cell types through the inference of GRNs and MDS. Author SummarySingle-cell omics technologies, such as single-cell RNA-seq (scRNA-seq), are instrumental in identifying novel cell subsets that are involved in various biological processes and diseases. These technologies, however, require further development in data analysis, especially in areas focused on cell-type identification and inference of interactions between genes. The problem of cell-type identification essentially involves clustering, which necessitates a balance between distinguishing different cell states and grouping similar ones together. Current clustering methods still suffer from uncertainty in determining the appropriate number of clusters and in explaining why some cells are clustered together but others are separated. The inference of interactions between genes, gene regulatory network (GRN), remains challenging due to the noisy nature of scRNA-seq. We have developed BootCellNet, a method that infers GRNs and a set of genes dominating the network dynamics and utilizes the set to cluster cells and identify cell types. The method addresses challenges in GRN identification and clustering methods simultaneously and will facilitate the generation of the working hypotheses from a large amount of scRNA-seq data.

bioinformatics↗

bioRxiv2023

Growth inhibitory factor/metallothionein-3 is a sulfane sulfur-binding protein

Cysteine-bound sulfane sulfur atoms in proteins have received much attention as key factors in cellular redox homeostasis. However, the role of sulfane sulfur in zinc regulation has been underinvestigated. We report here that cysteine-bound sulfane sulfur atoms serve as ligands to hold and release zinc ions in growth inhibitory factor (GIF)/metallothionein-3 (MT-3) with an unexpected C-S-S-Zn structure. Oxidation of such a zinc/persulfide cluster in Zn7GIF/MT-3 results in the release of zinc ions, and intramolecular tetrasulfide bridges in apo-GIF/MT-3 efficiently undergo S-S bond cleavage by thioredoxin to regenerate Zn7GIF/MT-3. Three-dimensional molecular modeling confirmed the critical role of the persulfide group in the thermostability and Zn-binding affinity of GIF/MT-3. The present discovery raises the fascinating possibility that the function of other Zn-binding proteins is controlled by sulfane sulfur.

biochemistry↗

bioRxiv2023

Multi-omics computational analysis unveils the in-volvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization

Macrophages display extreme plasticity, and the mechanisms and applications of polarization and de/repolarization of macrophages have been extensively investigated. However, the regulation of macrophage hysteresis de/repolarization remains unclear. In this study, by using a large-scale computational analysis of macrophage omics data, we report a list of hysteresis genes that maintain their expression patterns after polarization after ulti- and de/repolarization. While the polarization in M1 macrophages leads to a higher level of hysteresis in genes associated with cell cycle progression, cell migration, and enhancement of the immune response, we found weak levels of hysteresis after M2 polarization. During the polarization process from M0 to M1 and back to M0, the factors IRFs/STAT, AP-1, and CTCF regulate hysteresis by altering their binding sites to the chromatin. Overall, our results show that a history of polarization can lead to hysteresis in gene expression and chromatin changes over a given period. This study contributes to the understanding of de-/repolarization memory in macrophages.

bioinformatics↗

bioRxiv2023

Probe capture enrichment sequencing of amoA genes discloses diverse ammonia-oxidizing archaeal and bacterial populations

The ammonia monooxygenase subunit A (amoA) gene has been used to investigate the phylogenetic diversity, spatial distribution, and activity of ammonia-oxidizing archaeal (AOA) and bacterial (AOB), which contribute significantly to the nitrogen cycle in various ecosystems. Amplicon sequencing of amoA is a widely used method; however, it produces inaccurate results owing to the lack of a universal primer set. Moreover, currently available primer sets suffer from amplification biases, which can lead to severe misinterpretation. Although shotgun metagenomic and metatranscriptomic analyses are alternative approaches without amplification bias, the low concentration of target genes in heterogeneous environmental DNA restricts a comprehensive analysis to a realizable sequencing depth. In this study, we developed a method for amoA enrichment sequencing using a hybridization capture technique. Using metagenomic mock community samples, our approach effectively enriched amoA genes with low compositional changes, outperforming amplification and meta-omics sequencing analyses. Following the analysis of metatranscriptomic marine samples, we predicted 80 operational taxonomic units (OTUs) assigned to either AOA or AOB, of which 30 OTUs were unidentified using simple metatranscriptomic or amoA gene amplicon sequencing. Mapped read ratios to all the detected OTUs were significantly higher for the capture samples (50.4 {+/-} 27.2%) than for non-capture samples (0.05 {+/-} 0.02%), demonstrating the high enrichment efficiency of the method. The analysis also revealed the spatial diversity of AOA ecotypes with high sensitivity and phylogenetic resolution, which are difficult to examine using conventional approaches.

microbiology↗

bioRxiv2021

In planta genome editing with CRISPR/Cas9 ribonucleoproteins

In planta genome editing represents an attractive approach to engineering crops/varieties that are recalcitrant to culture-based transformation methods. Here, we report the direct delivery of CRISPR/Cas9 ribonucleoproteins into the shoot apical meristem using in planta particle bombardment and introduction of a semidwarf1 (sd1)-orthologous mutation into wheat. The triple knockout tasd1 mutant of an elite wheat variety reduced culm length by 10% without a reduction in yield.

plant biology↗

bioRxiv2017

Dynamic clustering of dynamin-amphiphysin rings regulates membrane constriction and fission coupled with GTP hydrolysis

Dynamin is a mechanochemical GTPase essential for membrane fission during clathrin mediated endocytosis. Dynamin forms washer ring-shaped/helical complexes at the neck of clathrin-coated pits and their structural changes coupled with GTP hydrolysis drive membrane fission. Dynamin and its binding protein amphiphysin cooperatively regulates membrane remodeling during fission, but its precise mechanism remains elusive. In this study, we analyze structural changes of dynamin-amphiphysin complexes during membrane fission using electron microscopy (EM) and high-speed atomic force microscopy (HS-AFM). Interestingly, HS-AFM analyses show that the dynamin-amphiphysin rings are rearranged to form clusters upon GTP hydrolysis and membrane constriction occurs at protein-uncoated regions flanking the clusters. We also show a novel function of amphiphysin in size control of the clusters to enhance biogenesis of endocytic vesicles. Our new approaches using combination of EM and HS-AFM clearly demonstrates dynamics of dynamin-amphiphysin complexes during membrane fission suggesting a novel \"clusterase\" model of dynamin-mediated membrane fission.

biophysics↗