Biology subjects

Kumamoto, T.

Publications and source records attributed to Kumamoto, T..

8 recordsLinked to original sources

bioRxiv2026

Mosaic evolution of avian brain compartments revealed by comparative MRI

Birds evolved large, cognitively capable forebrains independently of mammals, yet comparative analyses of avian brain organization have been constrained by the lack of standardized resources capable of resolving internal parcellation and long-range connectivity across species. Here, we present a comparative MRI resource spanning 16 avian species representing major clades and diverse ecological niches. We analyzed high-resolution T2-weighted and diffusion-weighted datasets suitable for direct interspecific comparison. T2-weighted morphometry revealed pronounced region-specific variation in internal brain architecture, including lineage-dependent differences in the relative prominence of major brain divisions and commissural structures, supporting a pattern of mosaic diversification rather than uniform scaling. To validate MRI-derived anatomical boundaries, we compared MRI parcellations with complementary histological analyses in three representative taxa (the large-billed crow, gentoo penguin, and mandarin duck), demonstrating close correspondence between MRI-defined borders and cytoarchitectonic transitions identified by Nissl staining, as well as major myelinated compartments visualized by Luxol Fast Blue staining. Moreover, diffusion MRI tractography and fractional anisotropy (FA) mapping further revealed both conserved and species-specific features of large-scale brain organization. Seed-based tractography of the optic lobe, dorsal cortex, cerebellum, and anterior cortex in chick, gentoo penguin, and large-billed crow revealed conserved within-compartment trajectory patterns alongside marked region-specific interspecific differences, particularly in optic-lobe-associated long-range trajectories. Whole-brain FA maps revealed complementary variation in regional microstructural organization across taxa. Together, this comparative MRI framework provides a cross-validated foundation for linking internal brain anatomy and long-range connectivity to ecological and evolutionary diversification in birds, with broader applications to comparative neuroanatomy across amniotes. Significance StatementHow does the internal architecture of the brain reorganize as species adapt to diverse lifestyles? Traditional comparative neuroanatomy has largely relied on overall brain size and external morphology, providing limited insight into internal subdivisions and long-range connectivity. In this study, we present a standardized avian MRI resource and a reproducible analytical pipeline that enables direct cross-species comparisons of 3D morphometry and diffusion-derived connectivity across 16 bird species representing major clades and diverse ecological niches. MRI-derived anatomical boundaries are validated through complementary histological analyses, providing biological support for cross-species parcellation and white-matter measurements. Using this framework, we demonstrate that avian brains diversify in a strongly mosaic manner, with region-and pathway-specific changes that vary disproportionately across lineages rather than scaling uniformly with overall brain size. By moving beyond simple correlations between brain size and behavior, this resource provides a benchmark for testing hypotheses of mosaic brain evolution and for linking neural architecture to ecological and behavioral diversification across vertebrates.

zoology↗

bioRxiv2026

Dual Developmental Origins and Activity-dependent Specification of Mammalian Subplate Neurons

Subplate neurons (SpNs) are among the earliest-generated cortical neurons and are essential for neocortical circuit assembly. Despite this central role, they have long been considered a mammalian innovation, yet their evolutionary origin remains unresolved. Here, using comparative single-cell and spatial transcriptomics across amniotes (mice, chicks, and turtles), we identify two distinct developmental and evolutionary origins of SpNs: atypical SpNs (aSpNs), an Nr4a2-negative population conserved across amniotes and originating from the medial pallium, and mammalian-type SpNs (mSpNs), an Nr4a2-positive population preferentially expanded in mammals and arising from early-born cortical neurons. Cross-species analyses show that early-born pallial neurons in non-mammalian amniotes differentiate into thalamic input neurons, whereas this ancestral program is repurposed in mammals, with early-born neurons transiently adopting a subplate identity. We further show that this fate switch is controlled by Zbtb18 repression linked to thalamic input. Collectively, these findings establish a dual-origin model for SpNs and provide a unifying framework for understanding neocortical evolution. One-Sentence SummaryDevelopmental rewiring of an ancestral input-neuron program gave rise to the mammalian subplate.

evolutionary biology↗

bioRxiv2026

BRCA2 loss triggers a downward spiral of genomic instability via ROS-dependent metabolic collapse

BRCA2 plays a central role in maintaining genome integrity through homologous recombination and replication-fork protection, yet the compensatory networks sustaining BRCA2-deficient cells remain unclear. Here we show BRCA2 enforces a homeostatic mechanism aligning mitochondrial respiration with DNA repair capacity in both cancer and non-cancer contexts. Genome-wide CRISPR screening identified glutathione metabolism and base-excision repair as the key compensatory networks sustaining BRCA2-deficient cells by detoxifying mitochondria-derived reactive oxygen species. BRCA2 loss provokes an acute mitochondrial ROS surge, causing 8-oxoguanine accumulation and a systemic metabolic crisis marked by NAD+ and glutathione depletion. PARP inhibitor targets DNA replication vulnerabilities, increasing the cellular requirement for BRCA2. The resulting oxidative burden primes cells for TP53-dependent apoptosis in G1 during olaparib treatment, which extends cytotoxicity beyond canonical S-phase stress. These findings indicate BRCA2 prevents metabolic flux from outpacing repair capacity, providing a rationale for combining PARP inhibition with redox modulation to enhance efficacy and overcome resistance. HighlightsO_LIAcute BRCA2 loss induces ROS and mitochondrial dysfunction creating a metabolic scar C_LIO_LIOxidative lesions drive PARP hyperactivation and precipitate a cellular NAD crisis C_LIO_LIPARP inhibitors provoke TP53-dependent apoptosis in G1 beyond replication stress in S phase C_LIO_LIGlutathione deficiency exacerbates bone marrow failure under BRCA2 depletion C_LIO_LIBRCA2 tightly couples mitochondrial redox homeostasis to genomic maintenance C_LI

cell biology↗

bioRxiv2025

Human-specific NOTCH2NL promotes astrogenesis by expanding proliferative glial progenitor states

The human cerebral cortex contains an unusually large number of glial cells, particularly astrocytes, yet the developmental and genetic mechanisms underlying their expansion remain poorly understood. While human-specific genes have been shown to promote neuronal production during cortical development, whether such genes also regulate gliogenesis has remained unclear. Here, we identify a previously unrecognized role for the human-specific gene family NOTCH2NL in promoting astrocyte-lineage expansion. Reanalysis of human fetal single-cell transcriptomic datasets revealed that NOTCH2NL is robustly expressed along the gliogenic trajectory, from glial intermediate progenitor cells to astrocytes. Functional perturbations in a human astrocyte culture system demonstrated that NOTCH2NL is both required and sufficient for astrocyte proliferation. In vivo overexpression of NOTCH2NLB in the developing mouse cortex shifted progenitor output toward the astrocyte lineage, increasing the astrocyte-to-neuron ratio from the early postnatal period through adulthood. This phenotype was associated with an expansion of proliferative glial progenitors around birth. Single-nucleus transcriptomic profiling further showed that NOTCH2NLB suppresses neuronal gene programs while activating transcriptional modules related to cell proliferation and cellular homeostasis during gliogenesis. Together, these findings indicate that human-specific NOTCH2NL acts at a conserved developmental decision point to amplify astrocyte production. Our study extends the function of NOTCH2NL beyond neurogenesis and suggests that human lineage-specific gene duplications can modulate gliogenesis, providing a developmental mechanism that may have contributed to the coordinated expansion of neuronal and glial populations in the human cortex.

developmental biology↗

bioRxiv2024

Conserved interhemispheric morphogenesis in amniotes preceded the evolution of the corpus callosum

The corpus callosum (CC) is the large axon bundle connecting the telencephalic hemispheres. The CC is formed exclusively in placental mammals, and the lack of comparable structures in other amniotes obscures the evolutionary origin of the CC. We here demonstrate that interhemispheric remodeling, a prior developmental step for CC formation, is highly conserved in non-mammalian amniotes, such as reptiles and birds. In these animal groups, the spatiotemporal dynamics of interhemispheric remodeling are tightly connected with distinct commissural formations. We observed a high degree of similarity between the mammalian CC and reptilian rostral pallial commissure, (RPC) and significant modifications in the avian pallial projection. Furthermore, we determined that Satb2 plays crucial roles in interhemispheric remodeling, which is associated with proper formation of both the CC and RPC in mice and geckoes, via the use of CRISPR-mediated gene-targeting. Our findings suggest that developmental mechanisms for midline remodeling were already present in the common ancestor of amniotes, which contributed to the evolution of eutherian-specific CC formation.

developmental biology↗

bioRxiv2023

Spatial transcriptome of developmental mouse brain reveals temporal dynamics of gene expressions and heterogeneity of the claustrum

During the development of the mammalian cerebral cortex, numerous neurons are arranged in a six-layer structure with an inside-out fashion to form the neocortex and wire neural circuits. This process includes cell proliferation, differentiation, migration, and maturation, supported by precise genetic regulation. To understand this sequence of processes at the cellular and molecular levels, it is necessary to characterize the fundamental anatomical structures by gene expression. However, markers established in the adult brain sometimes behave differently in the fetal brain, actively changing during development. Spatial transcriptomes yield genome-wide gene expression profiles from each spot patterned on tissue sections, capturing RNA molecules from fresh-frozen sections and enabling sequencing analysis while preserving spatial information. However, a deeper understanding of this data requires computational estimation, including integration with single-cell transcriptome data and aggregation of spots on the single-cell cluster level. The application of such analysis to biomarker discovery has only begun recently, and its application to the developing fetal brain is largely unexplored. In this study, we performed a spatial transcriptome analysis of the developing mouse brain to investigate the spatiotemporal regulation of gene expression during development. Using these data, we conducted an integrated study with publicly available mouse data sets, the adult brains spatial transcriptome, and the fetal brains single-cell transcriptome. Our data-driven analysis identified novel molecular markers of the choroid plexus, piriform cortex, thalamus, and claustrum. In addition, we revealed that the internal structure of the embryonic claustrum is composed of heterogeneous cell populations.

developmental biology↗

bioRxiv2022

Spontaneous and multifaceted ATP release from astrocytes at the scale of hundreds of synapses

Astrocytes participate in information processing by releasing neuroactive substances termed gliotransmitters, including ATP. Individual astrocytes come into contact with thousands of synapses with their ramified structure, but the spatiotemporal dynamics of ATP gliotransmission remain unclear, especially in physiological brain tissue. Using a genetically encoded fluorescent sensor, GRABATP1.0, we discovered that extracellular ATP increased locally and transiently in absence of stimuli in neuron-glia co-cultures, cortical slices, and the anesthetized mouse brain. Spontaneous ATP release events were tetrodotoxin-insensitive but suppressed by gliotoxin, fluorocitrate, and typically spread over 50-250 m2 area at concentrations capable of activating purinergic receptors. Besides, most ATP events did not coincide with Ca2+ transients. Clustering analysis revealed that these events followed multiple distinct kinetics, and blockade of exocytosis only decreased a minor group of slow events. Overall, astrocytes spontaneously release ATP through multiple mechanisms, mainly in non-vesicular and Ca2+-independent manners, thus potentially regulating hundreds of synapses all together.

neuroscience↗

bioRxiv2019

Direct readout of neural stem cell transgenesis with an integration-coupled gene expression switch

SUMMARYStable genomic integration of exogenous transgenes is critical for neurodevelopmental and neural stem cell studies. Despite the emergence of tools driving genomic insertion at high rates with DNA vectors, transgenesis procedures remain fundamentally hindered by the impossibility to distinguish integrated transgenes from residual episomes. Here, we introduce a novel genetic switch termed iOn that triggers gene expression upon insertion in the host genome, enabling simple, rapid and faithful identification of integration events following transfection with naked plasmids accepting large cargoes. In vitro, iOn permits rapid drug-free stable transgenesis of mouse and human pluripotent stem cells with multiple vectors. In vivo, we demonstrate accurate cell lineage tracing, assessment of regulatory elements and mosaic analysis of gene function in somatic transgenesis experiments that reveal new aspects of neural progenitor potentialities and interactions. These results establish iOn as an efficient and widely applicable strategy to report transgenesis and accelerate genetic engineering in cultured systems and model organisms.

developmental biology↗