Biology subjects

Koga, S.

Publications and source records attributed to Koga, S..

5 recordsLinked to original sources

bioRxiv2025

SpatialFinder: A Human-in-the-Loop Vision-Language Framework for Prioritizing High-Value Regions in Spatial Transcriptomics

Sequencing an entire spatial transcriptomics slide can cost thousands of dollars per assay, making routine use impractical. Focusing on smaller regions of interest (ROIs) based on adjacent routine H&E slides offers a practical alternative, but there is (i) no reliable way to identify the most informative areas from standard H&E images alone; and (ii) limited solutions for clinicians to prioritize the microenvironment of their own interests. Here we introduce SpatialFinder, a framework that combines a biomedical vision-language model (VLM) with a human-in-the-loop optimization pipeline to predict gene expression heterogeneity and rank high-value ROIs across routine H&E tissue slides. Evaluated across four Visium HD tissue types, SpatialFinder consistently outperforms baseline VLMs in selecting regions with high cellular diversity and tumor presence, achieving up to 89% correlation with ground truth rankings. These results demonstrate the potential of human-AI collaboration to make spatial transcriptomics more cost-effective and clinically actionable.

bioinformatics↗

bioRxiv2025

IL-25-induced memory ILC2s mediate long-term small intestinal adaptation

The adaptation of intestinal helminths to vertebrates evolved strategies to attenuate host tissue damage to support reproductive needs of parasites necessary to disseminate offspring to the environment. Helminths initiate the IL-25-mediated tuft cell-ILC2 circuit that enhances barrier protection of the host although viable parasites can target and limit the pathway. We used IL-25 to create small intestinal adaptation marked by anatomic, cell compositional and immunologic changes that persisted months after induction. Small intestinal adaptation was associated with heightened resistance to barrier pathogens, including in the lung, and sustained by transcriptionally and epigenetically modified, tissue-resident, memory-effector ILC2s distinct from those described by innate training; epithelial stem cells remained unaltered. Despite requiring IL-25 for induction, memory ILC2s maintained an activated state in the absence of multiple alarmins and supported mucosal resilience while avoiding adverse sensitization to chronic inflammation, revealing a pathway for deploying innate immune cells to coordinate a distributed mucosal defense.

immunology↗

bioRxiv2024

Identification of new resistance QTL regions in loquat cultivar Champagne against Pseudomonas syringae pv. eriobotryae group C

Loquat canker, caused by Pseudomonas syringae pv. eriobotryae, is a bacterial disease that infects loquat (Eriobotrya japonica) and has been reported in several countries. Three pathotypes, A, B, and C, have been reported in Japan. The loquat cultivar Champagne is resistant to the loquat canker group C and possesses a qualitative trait governed by a recessive homozygous pse-c gene located on Linkage Group 3 (LG3), and quantitative traits located at unidentified loci. In this study, we identified novel quantitative trait loci (QTL) regions for resistance to group C in this cultivar. A seedling population with Tanaka (Pse-c/Pse-c) crossed with Champagne (pse-c/pse-c) was tested. The genetic map of Champagne includes a total of 1,016 SNP markers mapped across 17 LGs, covering a total distance of 1,301 cM and an average marker density of 1.4 cM/locus. In addition to minor potential QTLs, the major QTL for resistance to loquat canker group C was detected in the upper region of LG14, with the QTL contributing 6.9% to the disease index. The results of this study open new possibilities for resistance breeding against this disease. Highlights.A total of 1,016 SNP markers were mapped on a linkage map consisting of 17 linkage groups with a total distance of 1,301 cM. QTL analysis revealed a novel resistance QTL region in Champagne against loquat canker group C in the upper part of the LG14. The identified QTLs in this study provide new possibilities for resistance breeding in loquat.

plant biology↗

bioRxiv2022

Quantitative live-cell imaging of secretion activity reveals dynamic immune responses

The measurement of cytokine secretions has contributed to the development of immunology; however, new methods that enable highly sensitive and efficient analysis are required for the precise characterisation of dynamic secretion activity when using rare cells or limited human specimens. Here, we report a new technology for quantitative live-cell imaging of secretion activity (qLCI-S), that enables high-throughput and dual-colour detection of prolonged secretion activity at the single-cell level, followed by transcriptome analysis for individual cells based on their phenotype. The power of the qLCI-S was demonstrated by visualising the individual and longitudinal cytokine secretion patterns of group 2 innate lymphoid cells, which comprised <0.01% human peripheral blood mononuclear cells, and identifying their minor subpopulations. This new technology will provide new insights into the spatiotemporal dynamic nature of various secretory functions and the development of fundamental tools for phenotypic drug discovery and regenerative and precision medicine.

biophysics↗

bioRxiv2021

Concurrent tau pathologies in frontotemporal lobar degeneration with TDP-43 pathology

AimsAccumulating evidence suggests that patients with frontotemporal lobar degeneration (FTLD) can have pathologic accumulation of multiple proteins, including tau and TDP-43. This study aimed to determine the frequency and characteristics of concurrent tau pathology in FTLD with TDP-43 pathology (FTLD-TDP). MethodsThe study included 146 autopsy-confirmed cases of FTLD-TDP and 55 cases of FTLD-TDP with motor neuron disease (FTLD-MND). Sections from the basal forebrain were screened for tau pathology with phospho-tau immunohistochemistry. For cases with tau pathology on the screening section, additional brain sections were studied to establish a diagnosis. Genetic analysis of C9ORF72, GRN, and MAPT was performed on select cases. ResultsAmong 201 cases, we found 72 cases (36%) with primary age-related tauopathy (PART), 85 (42%) with aging-related tau astrogliopathy (ARTAG), 45 (22%) with argyrophilic grain disease (AGD), and 2 cases (1%) with corticobasal degeneration (CBD). Patients with ARTAG or AGD were significantly older than those without these comorbidities. One of the patients with FTLD-TDP and CBD had C9ORF72 mutation and relatively mild tau pathology, consistent with incidental CBD. ConclusionThe coexistence of TDP-43 and tau pathologies was relatively common, particularly PART and ARTAG. Although rare, individual patients with FTLD can have multiple concurrent proteinopathies. The absence of TDP-43-positive astrocytic plaques may suggest that CBD and FTLD-TDP were independent disease processes in the two patients with both tau and TDP-43 pathologies. It remains to be determined if mixed cases represent a unique disease process or two concurrent disease processes in an individual.

pathology↗