Biology subjects

Kato, D.

Publications and source records attributed to Kato, D..

8 recordsLinked to original sources

bioRxiv2026

Bexobrutideg: A Selective, Catalytic Degrader of Bruton's Tyrosine Kinase Overcomes Inhibitor Resistance and Suppresses Autoantibody-Mediated Disease

Brutons tyrosine kinase (BTK) transduces B-cell receptor (BCR), Toll-like receptor (TLR), and Fc receptor (FcR) signaling, and overactivation of these pathways drives B-cell malignancies and antibody-mediated autoimmune disease. Small molecule inhibitors block the enzymatic functions of BTK, but this inhibition is undermined by resistance mutations, several of which abolish BTKs kinase activity yet promote oncogenic signaling through BTK scaffolding functions. We report the discovery and characterization of bexobrutideg (NX-5948), a heterobifunctional degrader that recruits cereblon (CRBN) to selectively degrade BTK while sparing molecular glue neosubstrates. We demonstrate that bexobrutideg acts catalytically, degrading thousands of copies of BTK per molecule per hour, and this event-driven pharmacology renders it resilient to mutations that confer resistance to both covalent- and noncovalent-inhibitors. Bexobrutideg is orally bioavailable, driving deep and durable BTK degradation across species. Bexobrutideg demonstrates strong efficacy in wild-type and ibrutinib-resistant lymphoma models and robustly suppresses pathway activation in models of autoimmune disease.

cancer biology↗

bioRxiv2026

Macrophages target PVR/CD155 on colorectal cancer cells via REVERBalpha

Background&AimsPatients with microsatellite-instable (MSI) colorectal cancer (CRC) benefit from immune checkpoint therapy. For patients with microsatellite-stable (MSS) non-MSI tumors targeting alternative immune checkpoints, such as the Poliovirus receptor (PVR/CD155), may extend response to checkpoint inhibitors and thereby improve outcomes. The drugable transcription factor REVERB (NR1D1) is a master repressor of macrophage function. We hypothesized that regulation of PVR allows elimination of tumor cells by macrophage-directed precision therapy. MethodsHuman CRC cell lines (MSS+: HT29, SW480; MSI+: HCT116), patient-derived organoids (MSS+ PDOs) and tissues were assessed by PCR, Western blot, immunohistochemistry and flow cytometry. 3D co-cultures of CRC cells with macrophages derived from THP1 monocytic leukemia cells or peripheral blood of healthy donors were analysed by microscopy and viability assays. Functional perturbation of PVR and REVERB was achieved by CRISPR/Cas9-sgRNA gene modification, synthetic ligands or blocking antibodies (Abs). ResultsREVERB bound a cognate DNA-element in the -1 kb human PVR gene promoter, and its agonist (SR9009) super-repressed, whereas its antagonist (SR8278) de-repressed transcription of PVR mRNA in macrophages. Macrophages with CRISPR-modified REVERB were unresponsive to ligand, devoid of PVR protein, showed more phagocytosis, tumor cell efferocytosis and expression of genes related to host immunity (PDL1, TLR4 e.a.) than clones with the wild-type receptor. Macrophages lowered the viability of tumor cells, potentiated by PVR blocking Ab or PVR knock-out in tumor cells. Consistently, REVERB antagonist augmented tumor cell death in co-cultures with macrophages and PVR blocking Ab. ConclusionCo-addressing the checkpoint axis REVERB-PVR may represent a novel intervention strategy for patients with MSS+ CRC.

cancer biology↗

bioRxiv2024

Unsupervised deep learning enables blur-free super-resolution in two-photon microscopy

We developed an unsupervised deep learning method to simultaneously perform deblurring, super-resolution, and segmentation of two-photon microscopy images. Two-photon microscopy is an excellent technique for non-invasively observing deep biological tissues, but blurring during deep imaging has been a challenge. Conventional deblurring methods have limited performance and are not suitable for deblurring two-photon microscopy images. Moreover, methods that simultaneously perform segmentation, which is usually required in downstream analysis, have not been developed. Therefore, in this method (TENET), we precisely modeled the blur of two-photon microscopy and simultaneously achieved deblurring, super-resolution, and segmentation through unsupervised deep learning. In simulation and experimental data, we achieved deblurring, resolution improvement, and segmentation accuracy surpassing conventional methods. Furthermore, we applied the method to live imaging of microglia, enabling quantitative 3D morphological analysis that was previously difficult. This method allows non-invasive visualization of detailed structures in deep biological tissues, and is expected to lead to a more high-definition understanding of biological phenomena. Future applications to time-series morphological analysis of microglia are anticipated.

bioinformatics↗

bioRxiv2023

Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade

The Clostridia is a dominant bacterial class in the guts of various animals and are considered to nutritionally contribute to the animal host. Here, we discovered clostridial endosymbionts of cellulolytic protists in termite guts, which have never been reported with evidence. We obtained (near-)complete genome sequences of three endosymbiotic Clostridia, each associated with a different parabasalid protist species with various infection rates: Trichonympha agilis, Pseudotrichonympha grassii, and Devescovina sp. All these protists are previously known to harbor permanently-associated, mutualistic Endomicrobia or Bacteroidales that supplement nitrogenous compounds. The genomes of the endosymbiotic Clostridia were small in size (1.0-1.3 Mbp) and exhibited signatures of an obligately-intracellular parasite, such as an extremely limited capability to synthesize amino acids, cofactors, and nucleotides and a disrupted glycolytic pathway with no known net ATP-generating system. Instead, the genomes encoded ATP/ADP translocase and, interestingly, regulatory proteins that are unique to eukaryotes in general and are possibly used to interfere with host cellular processes. These three genomes formed a clade with metagenome-assembled genomes (MAGs) derived from the guts of other animals, including human and ruminants, and the MAGs shared the characteristics of parasites. Gene flux analysis suggested that the acquisition of the ATP/ADP translocase gene in a common ancestor was probably key to the emergence of this parasitic clade. Taken together, we provide novel insights into the multilayered symbiotic system in the termite gut by adding the presence of parasitism and present an example of the emergence of putative energy parasites from a dominant gut bacterial clade.

microbiology↗

bioRxiv2023

Transcriptome analysis of peripheral blood of Schistosoma mansoni infected children from the Albert Nile region in Uganda reveals genes implicated in fibrosis pathology.

Over 290 million people are infected by schistosomes worldwide. Schistosomiasis control efforts focus on mass drug treatment with praziquantel (PZQ), a drug that kills the adult worm of all Schistosoma species. Nonetheless, re-infections have continued to be detected in endemic areas with individuals living in the same area presenting with varying infection intensities. Our objective was to characterize the transcriptome profiles in peripheral blood of children between 10 - 15 years with varying intensities of Schistosoma mansoni infection living along the Albert Nile in Uganda. RNA extracted from peripheral blood collected from 44 S. mansoni infected (34 high and 10 low by circulating anodic antigen [CAA] level) and 20 uninfected children was sequenced using Illumina NovaSeq S4 and the reads aligned to the GRCh38 human genome. Differential gene expression analysis was done using DESeq2 and enriched pathways in differentially expressed genes (DEGs) were identified using REACTOME. Principal component analysis revealed clustering of gene expression by gender when S. mansoni infected children were compared with uninfected children. In addition, we identified 14 DEGs between S. mansoni infected and uninfected individuals, 56 DEGs between children with high infection intensity and uninfected individuals, 33 DEGs between those with high infection intensity and low infection intensity and no DEGs between those with low infection and uninfected individuals. We also observed upregulation and downregulation of some DEGs that are associated with fibrosis and its regulation. These data suggest expression of fibrosis associated genes as well as genes that regulate fibrosis in S. mansoni infection. The relatively few significant DEGS observed in children with schistosomiasis suggests that chronic S. mansoni infection is a stealth infection that does not stimulate a strong immune response. Author SummarySchistosomiasis is a neglected tropical disease transmitted via an intermediate snail host through contact with contaminated fresh water. Even with routine Mass Drug Administration for treatment of the infection, re-infections are still common and variations in infection intensity and pathology are still observed in individuals in the same location. These may be due to differences in individuals response to S. mansoni infection. In this study, we used RNAseq to identify differentially expressed genes associated with S. mansoni infection in children between 10-15 years. We conducted comparisons between phenotypes including infection intensities measured by circulating anodic antigen, wasting by body mass index and stunting by height-for-age z score. Our data showed very low numbers of significant differentially expressed genes in all comparisons. Some of the few differentially expressed genes that were observed were associated with fibrosis which is the cause of pathology in humans and has been observed in late stages of S. mansoni infection in murine studies.

genomics↗

bioRxiv2022

Analysis of the Toll and spaetzle genes involved in Toll path-way-dependent antimicrobial gene induction in the red flour beetle, Tribolium castaneum (Coleoptera: Tenebriodae)

Insects rely only on their innate immune system to protect themselves from pathogens. Antimicrobial peptide (AMP) production is the main immune reaction in insects. In Drosophila melanogaster, the reaction is regulated mainly by the Toll and immune deficiency (IMD) pathways. Spaetzle proteins, activated by immune signals from upstream components, bind to Toll proteins, thus activating the Toll pathway, which in turn induces AMP genes. Previous studies have shown the difference immune ststems related to Toll and IMD pathways between D. melanogaster and Tribolium castaneum. In T. castaneum, 9 Toll and 7 spaetzle genes have been identified. To extend our understanding of AMP production by T. castaneum, we conducted functional assays of Toll and spaetzle genes related to Toll pathway-dependent AMP gene expression in T. castaneum under challenge with bacteria or budding yeast using RNA interference and qRT-PCR. The results revealed that Toll3 and Toll4 double-knockdown and spz7 knockdown strongly and moderately reduced the Toll pathway-dependent expression of AMP genes, respectively. Moreover, Toll3 and Toll4 double-knockdown pupae more rapidly succumbed to entomopathogenic bacteria than the control pupae, but spz7 knockdown pupae did not. The results suggest that Toll3 and Toll4 play a large role in Toll pathway-dependent immune reactions, whereas spz7 plays a small part.

molecular biology↗

bioRxiv2022

Border-associated macrophages transventricularly infiltrate the early embryonic cerebral wall to differentiate into microglia

The relationships between microglia and macrophages, especially their lineage segregation outside the yolk sac, have been recently explored, providing a model in which a conversion from macrophages seeds microglia during brain development. However, spatiotemporal evidence to support such microglial seeding and to explain how it occurs has not been obtained. By cell tracking via slice culture, intravital imaging, and Flash tag-mediated labeling, we found that a group of intraventricular macrophages belonging to border-associated macrophages (BAMs), which were abundantly observed along the inner surface of the mouse cerebral wall at embryonic day 12, frequently entered the brain wall. Immunohistochemistry of the tracked cells showed that postinfiltrative BAMs acquired microglial properties while losing a macrophage phenotype. We also found that the intraventricular BAMs were supplied transepithelially from the roof plate. Thus, this study demonstrates that the "roof plate[->]ventricle[->]cerebral wall" route is an essential path for microglial colonization into the embryonic mouse brain.

neuroscience↗

bioRxiv2019

Structural Studies of Overlapping Dinucleosomes in Solution

An overlapping dinucleosome (OLDN) is a structure composed of one hexasome and one octasome and appears to be formed through nucleosome collision promoted by nucleosome remodeling factor(s). In the present study, the solution structure of the OLDN was investigated through integration of small-angle X-ray and neutron scattering (SAXS and SANS, respectively), computer modeling, and molecular dynamics simulations. Starting from the crystal structure, we generated a conformational ensemble based on normal mode analysis, and searched for the conformations that well reproduced the SAXS and SANS scattering curves. We found that inclusion of histone tails, which are not observed in the crystal structure, greatly improved model quality. The obtained structural models suggest that OLDNs adopt a variety of conformations stabilized by histone tails situated at the interface between the hexasome and octasome, simultaneously binding to both the hexasomal and octasomal DNA. In addition, our models define a possible direction for the conformational changes or dynamics, which may provide important information that furthers our understanding of the role of chromatin dynamics in gene regulation.\n\nStatement of SignificanceOverlapping dinucleosomes (OLDNs) are intermediate structures formed through nucleosome collision promoted by nucleosome remodeling factor(s). To study the solution structure of OLDNs, a structural library containing a wide variety of conformations was prepared though simulations, and the structures that well reproduced the small angle X-ray and neutron scattering data were selected from the library. Simultaneous evaluation of the conformational variation in the global OLDN structures and in the histone tails is difficult using conventional MD simulations. We overcame this problem by combining multiple simulation techniques, and showed the importance of the histone tails for stabilizing the structures of OLDNs in solution.

biophysics↗