Biology subjects

Miyagishima, D.

Publications and source records attributed to Miyagishima, D..

3 recordsLinked to original sources

bioRxiv2026

Multicellular Spatial Programs Define the Histopathological Architecture of Meningioma

Tumors are often described by cell types or gradients, but the organizing units of tumor tissue remain unclear. Using meningiomas, which show marked morphologic diversity despite constrained and recurrent genetics, we identify reproducible multicellular spatial molecular programs (SMPs) characterized by recurring cell-type mixtures that combine in different proportions across tumors. We built a multi-omic atlas of 147 human meningiomas (1.6 million cells/spots), integrating scRNA-seq, Visium, CosMx-RNA, and CosMx-Protein. Across platforms, SMPs mapped onto canonical whorl-lobule architecture and defined a structured ecological landscape linking hypoxic, immune-evasive states to vascularized, matrix-remodeling, and mineralization-rich states. For translation, we developed MeningNet, a hybrid ConvNeXt-Vision Transformer that infers SMPs directly from hematoxylin-and-eosin sections. MeningNet generalized across an internal replication cohort and 465 external whole-slide images, recovering cross-platform inference and showing significant association with CNS-WHO grade. These findings establish meningioma architecture as a reproducible histopathological framework for inferring spatial molecular state from routine pathology.

Cancer Biology↗

bioRxiv2025

Non-invasive approach for endoluminal biopsy coupled with single-cell proteomics allows for immune characterization of intracranial aneurysms

The immune regulatory mechanisms driving the stability, growth, and rupture of intracranial aneurysms (IAs) remain incompletely understood. In this study, we employ endoluminal biopsy with single-cell proteomics to comprehensively profile the immune landscape of IAs across their pathologic states. Our findings reveal distinct immune signatures associated with aneurysm states. Stable, i.e. non-growing unruptured, IAs exhibit a balanced immune cell composition. Ruptured IAs are marked by significant neutrophil predominance. Notably, we highlight key immune markers in aneurysm instability, offering new insights into immune drivers of aneurysm progression. These findings provide a foundation for immune-targeted, non-invasive therapeutic strategies aimed at targeting IAs and preventing rupture.

physiology↗

bioRxiv2022

spARC Recovers Human Glioma Spatial SignalingNetworks with Graph Filtering

Biological networks operate within architectural frameworks that influence the state and function of cells through niche-specific factors such as exposure to nutrients and metabolites, soluble signaling molecules, and direct cognate cell-cell communication. Spatial omics technologies incorporate environmental information into the study of biological systems, where the spatial coordinates of cells may directly or indirectly encode these micro-anatomical features. However, they suffer from technical artifacts, such as dropout, that impede biological discovery. Current methods that attempt to correct for this fail to adequately integrate highly informative spatial information when recovering gene expression and modelling cell-cell dynamics in situ. To address this oversight, we developed spatial Affinity-graph Recovery of Counts (spARC), a data diffusion-based filtration method that shares information between neighboring cells in tissue and related cells in expression space, to recover gene dynamics and simulate signalling interactions in spatial transcriptomics data. Following validation, we applied spARC to 10 IDH-mutant surgically resected human gliomas across WHO grades II-IV in order to study signaling networks across disease progression. This analysis revealed co-expressed genes that border the interface between tumor and tumor-infiltrated brain, allowing us to characterize global and local structure of glioma. By simulating paracrine signaling in silico, we identified an Osteopontin-CD44 interaction enriched in grade IV relative to grade II and grade III astrocytomas, and validated the clinical relevance of this signaling axis using TCGA.

bioinformatics↗