Biology subjects

Kudo, H.

Publications and source records attributed to Kudo, H..

7 recordsLinked to original sources

bioRxiv2026

A microbiota-responsive polyfunctional cytotoxic CD4⁺ T-cell state promotes mucosal inflammation in ulcerative colitis

Ulcerative colitis (UC) is characterised by chronic colonic inflammation with marked heterogeneity in disease severity and therapeutic outcomes. Here, we define a spatially organised, polyfunctional cytotoxic CD4 T-cell state associated with mucosal inflammation and adverse therapeutic outcomes in UC. Integrating ex vivo T-cell receptor stimulation with multi-cohort bulk and single-cell transcriptomics and multiparameter flow cytometry, we show that GZMB CD4 T cells are preferentially enriched in inflamed UC mucosa, but not peripheral blood, and co-express cytotoxic molecules, Th1- and Th17-associated cytokines and chemokines, and immunoregulatory receptors. Single-cell analyses implicate inflammatory cytokine and antigen-presentation signals in the acquisition or maintenance of this state. High-resolution spatial profiling localised this programme predominantly to Th17 cells, which were preferentially enriched within multicellular inflammatory and tertiary lymphoid structure-associated niches. Across independent patient cohorts, a transcriptional signature derived from this state increased with endoscopic disease severity and was associated with reduced response to anti-TNF and anti-IL-12/23p40 therapies. Adoptive transfer of Gzma/Gzmb-deficient rather than wild-type CD4 T cells into Rag2-deficient recipient mice markedly attenuated experimental colitis and abrogated the polyfunctional cytokine phenotype, demonstrating that granzyme-dependent effector activity is a key mechanism driving CD4+ T-cell-mediated intestinal inflammation. Finally, human host-microbiome analysis linked this programme to intestinal dysbiosis, while transfer of dysbiotic microbiota promoted the emergence of a corresponding state in vivo. Collectively, these findings define a microbiota-responsive, spatially organised polyfunctional cytotoxic CD4 T-cell programme that contributes to intestinal inflammation and is associated with disease severity and treatment resistance in UC.

immunology↗

bioRxiv2026

A dysregulated stromal remodelling programme characterises prior anti-TNF failure in ulcerative colitis

Prior anti-tumour necrosis factor (TNF) failure is associated with reduced efficacy of subsequent advanced therapies in ulcerative colitis (UC), but the biological basis of this treatment-refractory state remains unclear. We integrated clinical outcomes and baseline colonic transcriptomic data from UC patients in the UNIFI phase III trial programme with regulatory and signalling network inference, connectivity mapping, and single-cell-resolution spatial transcriptomics. Colonic transcriptomic analyses identified coordinated enrichment of extracellular matrix organisation, collagen remodelling and integrin-associated programmes, increased stromal cell representation and elevated inferred MAPK/EGFR activity in UC patients with prior anti-TNF failure. Causal network inference prioritised MAPK3 as a candidate regulator of this state, while connectivity mapping identified MEK/EGFR inhibitors as candidate perturbagens. MEK inhibition suppressed stromal pathways and reduced inferred MAPK/EGFR activity ex vivo. Spatial profiling of active UC and non-IBD colonic tissues localised these programmes to UC-enriched stromal niches. Ligand-receptor inference further identified reciprocal stromal-myeloid communication within these niches. Collectively, these findings define a stromal remodelling programme associated with prior anti-TNF failure and nominate MAPK/EGFR signalling as a potentially tractable component of treatment-refractory UC.

systems biology↗

bioRxiv2022

Structure and Function of Gli123 Involved in Mycoplasma mobile Gliding

Mycoplasma mobile is a fish pathogen that glides on solid surfaces by means of a unique mechanism. The gliding machinery of M. mobile is composed of internal and surface structures. In the present study, we focused on the function and structure of Gli123, a surface protein that is essential for the localization of other surface proteins. The amino acid sequence of Gli123, which is 1128 amino acids long, contains lipoprotein-specific repeats. We isolated the native Gli123 protein from M. mobile cells and a recombinant protein, rGli123, from Escherichia coli. The isolated rGli123 complemented a non-binding and non-gliding mutant of M. mobile that lacked Gli123. Circular dichroism and rotary-shadowing electron microscopy (EM) showed that rGli123 has a structure that is not significantly different from that of the native protein. Rotary-shadowing EM suggested that the molecules changed their shape between globular and rod-like structures, depending on the ionic strength of the solution. Negative-staining EM coupled with single-particle analysis revealed that Gli123 forms a globular structure featuring a small protrusion with dimensions of 20.0, 14.5, and 16.0 nm. Small-angle X-ray scattering analyses indicated a rod-like structure composed of several tandem globular domains with total dimensions of approximately 34 nm length and 4 nm width. Both molecular structures were suggested to be dimers based on the predicted molecular size and structure. Gli123 may have evolved by multiplication of repeating lipoprotein units and acquired clumping role of surface proteins. IMPORTANCEMycoplasmas are pathogenic bacteria that are widespread in animals. They are characterized by small cell and genome sizes but are equipped with unique abilities to escape host immunity, such as surface variation and gliding. Here, we focused on a surface-localizing protein that is essential for Mycoplasma mobile gliding. The findings of this study suggested that the protein undergoes drastic conformational changes between its rod-like and globular structures. These changes may be caused by a repetitive structure common in the surface proteins that is responsible for the modulation of the cell surface structure and related to the assembly process for the surface gliding machinery. An evolutionary process for this unique mycoplasma gliding mechanism has also been suggested in the present study.

microbiology↗

bioRxiv2020

Cryptic promoter activation occurs by at least two different mechanisms in the Arabidopsis genome

In gene-trap screening of plant genomes, promoterless reporter constructs are often expressed without trapping of annotated gene promoters. The molecular basis of this phenomenon, which has been interpreted as the trapping of cryptic promoters, is poorly understood. In this study, using Arabidopsis gene-trap lines in which a firefly luciferase (LUC) open reading frame (ORF) was expressed from intergenic regions, we found that cryptic promoter activation occurs by at least two different mechanisms: one is the capturing of pre-existing promoter-like chromatin marked by H3K4me3 and H2A.Z, and the other is the entirely new formation of promoter chromatin near the 5 end of the inserted LUC ORF. To discriminate between these, we denoted the former mechanism as "cryptic promoter capturing", and the latter one as "promoter de novo origination". The latter finding raises a question as to how inserted LUC ORF sequence is involved in this phenomenon. To examine this, we performed a model experiment with chimeric LUC genes in transgenic plants. Using Arabidopsis psaH1 promoter-LUC constructs, we found that the functional core promoter region, where transcription start sites (TSS) occur, cannot simply be determined by the upstream nor core promoter sequences; rather, its positioning proximal to the inserted LUC ORF sequence was more critical. This result suggests that the insertion of the LUC ORF sequence alters the local distribution of the TSS in the plant genome. The possible impact of the two types of cryptic promoter activation mechanisms on plant genome evolution and endosymbiotic gene transfer is discussed.

evolutionary biology↗

bioRxiv2020

Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs

BackgroundIncreasing the power of genome-wide association studies in diverse populations is important for understanding the genetic determinants of disease risks, and large-scale genotype data are collected by genome cohort and biobank projects all over the world. In particular, ethnic-specific SNP arrays are becoming more important because the use of universal SNP arrays has some limitations in terms of cost-effectiveness and throughput. As part of the Tohoku Medical Megabank Project, which integrates prospective genome cohorts into a biobank, we have been developing a series of Japonica Arrays for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population. ResultsWe designed a novel version of the SNP Array for the Japanese population, called Japonica Array NEO, comprising a total of 666,883 SNPs, including tag SNPs of autosomes and X chromosome with pseudoautosomal regions, SNPs of Y chromosome and mitochondria, and known disease risk SNPs. Among them, 654,246 tag SNPs were selected from an expanded reference panel of 3,552 Japanese using pairwise r2 of linkage disequilibrium measures. Moreover, 28,298 SNPs were included for the evaluation of previously identified disease risk SNPs from the literature and databases, and those present in the Japanese population were extracted using the reference panel. The imputation performance of Japonica Array NEO was assessed by genotyping 286 Japanese samples. We found that the imputation quality r2 and INFO score in the minor allele frequency bin >2.5%-5% were >0.9 and >0.8, respectively, and >12 million markers were imputed with an INFO score >0.8. After verification, Japonica Arrays were used to efficiently genotype cohort participants from the sample selection to perform a quality assessment of the raw data; approximately 130,000 genotyping data of >150,000 participants has already been obtained. ConclusionsJaponica Array NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores for this population and further identifying disease risk alleles among individuals of East Asian ancestry.

genomics↗

bioRxiv2019

Stat2 loss disrupts damage signalling and is protective in acute pancreatitis

Severity of sterile inflammation, as seen in acute pancreatitis, is determined by damage-sensing receptors, signalling cascades and cytokine production. Stat2 is a type I interferon signalling mediator that also has interferon-independent roles in murine lipopolysaccharide-induced NF-{kappa}B-mediated sepsis. However its role in sterile inflammation is unknown. We hypothesised that Stat2 determines severity of non-infective inflammation in the pancreas.\n\nWild type (WT) and Stat2-/- mice were injected intraperitoneally with cerulein or L-arginine. Specific cytokine-blocking antibodies were used in some experiments. Pancreata and blood were harvested 1h and 24h after the final dose of cerulein and up to 96h post L-arginine. Whole-tissue phosphoproteomic changes were assessed using label-free mass spectrometry. Tissue-specific Stat2 effects were studied in WT/Stat2-/- bone-marrow chimera and using Cre-lox recombination to delete Stat2 in pancreatic and duodenal homeobox 1(Pdx1)-expressing cells.\n\nStat2-/- mice were protected from cerulein- and L-arginine-induced pancreatitis. Protection was independent of type I interferon signalling. Stat2-/- mice had lower cytokine levels including TNF and IL-10 and reduced NF-kB nuclear localisation in pancreatic tissue compared to WT. Inhibition of TNF improved (inhibition of IL-10 worsened) cerulein-induced pancreatitis in WT but not Stat2-/- mice. Phosphoproteomics showed down-regulation of mitogen-activated protein kinase (MAPK) mediators but accumulation of Ser412-phosphorylated Tak1. Stat2 deletion in Pdx1-expressing acinar cells (Stat2flox/Pdx1-cre) reduced pancreatic TNF expression, but not histological injury or serum amylase. WT/Stat2-/- bone-marrow chimera were protected from pancreatitis irrespective of host or recipient genotype.\n\nStat2 loss results in disrupted signalling in pancreatitis, upstream of NF-{kappa}B in non-acinar and/or bone marrow derived cells.

immunology↗

bioRxiv2017

Network analysis of mass spectrometry imaging data from colorectal cancer identifies key metabolites common to metastatic development.

A deeper understanding of inter-tumor and intra-tumor heterogeneity is a critical factor for the advancement of next generation strategies against cancer. The heterogeneous morphology exhibited by solid tumors is mirrored by their metabolic heterogeneity. Defining the basic biological mechanisms that underlie tumor cell variability will be fundamental to the development of personalized cancer treatments. Variability in the molecular signatures found in local regions of cancer tissues can be captured through an untargeted analysis of their metabolic constituents. Here we demonstrate that DESI mass spectrometry imaging (MSI) combined with network analysis can provide detailed insight into the metabolic heterogeneity of colorectal cancer (CRC). We show that network modules capture signatures which differentiate tumor metabolism in the core and in the surrounding region. Moreover, module preservation analysis of network modules between patients with and without metastatic recurrence explains the inter-subject metabolic differences associated with diverse clinical outcomes such as metastatic recurrence.\n\nSignificanceNetwork analysis of DESI-MSI data from CRC human tissue reveals clinically relevant co-expression ion patterns associated with metastatic susceptibility. This delineates a more complex picture of tumor heterogeneity than conventional hard segmentation algorithms. Using tissue sections from central regions and at a distance from the tumor center, ion co-expression patterns reveal common features among patients who developed metastases (up of > 5 years) not preserved in patients who did not develop metastases. This offers insight into the nature of the complex molecular interactions associated with cancer recurrence. Presently, predicting CRC relapse is challenging, and histopathologically like-for-like cancers frequently manifest widely varying metastatic tendencies. Thus, the methodology introduced here more robustly defines the risk of metastases based on tumor biochemical heterogeneity.\n\nAuthor contributionsP.I., Z.T., R.C.G.: designed the study, developed the workflow, analyzed the data, interpreted the results, wrote the paper; N.S. collected the MS, performed the H...E staining, wrote the paper; L.D.: interpreted the results, wrote the paper; A.M.: collected the MS; A.S.: histological assessment; L.P.: collected the tissue specimens and clinical metadata; A.D.: collected the MS; H.K.: performed the H...E staining; R.M.: collected the tissue specimens and clinical metadata. R.G.: histological assessment; J.K.N: designed the study, edited the paper.

cancer biology↗