Biology subjects

Nishitani, K.

Publications and source records attributed to Nishitani, K..

8 recordsLinked to original sources

bioRxiv2026

Spatial transcriptomics identifies L6 corticothalamic and L6b subplate-like heterotopic neurons in an epileptogenic SLC35A2-associated brain malformation.

Increased white matter (WM) heterotopic neurons are a pathological feature observed in various neurological and psychiatric disorders. Mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE) is a drug-resistant epilepsy-associated cortical malformation characterized by increased WM heterotopic neurons and OLIG2-positive cells and frequently associated with somatic SLC35A2 mutations. However, the precise cellular identity of these heterotopic neurons remains unclear. Using imaging-based spatial transcriptomics (iST) of SLC35A2-mutated MOGHE tissues, we found that most WM heterotopic neurons exhibited molecular signatures of excitatory neurons. Further analyses revealed that these heterotopic excitatory neurons included prominent populations with layer 6 corticothalamic (CT)-like and layer 6b subplate neuron (SpN)-like molecular features. These findings were further supported by human immunohistochemistry and a Slc35a2 conditional knockout (cKO) mouse model. Together, our results provide a cellular characterization of WM heterotopic neurons in MOGHE and suggest a new perspective on disease pathophysiology centered on deep-layer excitatory neuronal populations.

neuroscience↗

bioRxiv2026

MLL3 adaptor function, not methyltransferase catalytic activity, is essential for breast tumor suppression

MLL3 (Mixed-Lineage Leukemia 3), also known as KMT2C, is one of the most frequently altered epigenetic regulators in breast cancer. MLL3 loss-of-function leads to accelerated tumor onset and growth and increased metastasis. As a large multi-domain protein, MLL3 functions as a histone methyltransferase and a nuclear protein adaptor interacting with other epigenetic proteins. Since breast cancer MLL3 mutations are often truncating mutations that lead to protein degradation, whether the MLL3 tumor suppressor activity depends on its catalytic activity or non-catalytic chromatin adaptor function remains unclear. Here, using CRISPR genetically engineered mouse mammary stem cell organoid-based breast tumor models, we dissected dosage-dependent and domain-specific functions of MLL3 in breast tumor suppression. MLL3 heterozygous loss breast tumor models revealed that MLL3 is haplo-insufficient for breast tumor suppression. Interestingly, homozygous catalytic-dead MLL3-Y4792A mutation did not accelerate tumor onset, growth, or metastasis. By contrast, G367V mutation in the PHD2 domain, which disrupts the BAP1 complex binding without affecting MLL3 protein stability, accelerated tumor onset and growth, phenocopying MLL3 loss. Mechanistically, MLL3 loss impaired chromatin localization of UTX, and genetic depletion of UTX accelerated breast tumor progression in MLL3-wildtype but not MLL3-deficient cells. Integrated RNA-seq, CUT&TAG, and ATAC-seq analyses further showed that transcriptional changes induced by MLL3 loss were more closely associated with promoter-proximal alterations in H3K27Ac, H3K27me3, and chromatin accessibility than with putative MLL3-dependent enhancer regions. Together, these findings reveal that MLL3 suppresses breast tumor initiation through a dosage-sensitive, catalytic-independent adaptor function that regulates promoter-proximal epigenetic states.

cancer biology↗

bioRxiv2026

Comprehensive transcriptomic and proteomic profiling of mTOR-related epilepsy

Malformations of cortical development (MCDs) are a major cause of drug-resistant epilepsy (DRE) in children. A subset of MCDs, including focal cortical dysplasia type II, tuberous sclerosis complex, and hemimegalencephaly, shares characteristic histopathological features and somatic mutations in genes within the PI3K-AKT-mTOR signaling cascade, and is termed mTORopathies. However, the molecular mechanisms that drive epileptogenesis and consequent uncontrollable seizures in these disorders remain poorly understood. Here, we performed integrated genomic, transcriptomic, and proteomic analyses of 60 surgical brain specimens from 42 patients with MCDs and 18 with mesial temporal lobe epilepsy. Targeted genomic sequencing identified 19 somatic mutations in PI3K-AKT-mTOR pathway genes, including novel variants in AKT3 (L51H) and MTOR (A512T). RNA sequencing comparing mTORopathy brains with controls, along with cross-validation using an independent public dataset, identified 287 consistently differentially expressed genes that were consistently altered. Downregulated genes were enriched in oxidative phosphorylation (OXPHOS) and mitochondrial metabolic pathways, whereas upregulated genes were associated with gliogenesis and cellular senescence. Proteomic profiling identified 44 differentially expressed proteins, including significant reductions in OXPHOS-related proteins (COX5B, NDUFS4, GOT2, RAB27B, and DKK3). Our study provides a patient-matched, multi-omics dataset of human mTOR-related epilepsies from a single-institution cohort. Integrated analyses across transcriptomic and proteomic layers highlight impairment of OXPHOS as a molecular hallmark of mTORopathies, Integrated transcriptomic and proteomic analyses identified impaired OXPHOS as a molecular hallmark, potentially contributing to focal hypometabolism in mTORopathy. These findings offer mechanistic insights into epileptogenesis and provide a valuable resource for understanding molecular pathologies and developing mechanism-based therapies for mTOR-related epilepsy.

neuroscience↗

bioRxiv2026

Single-cell-resolved spatial multi-omics identifies mTOR-driven neuronal and astroglial pathogenicity underlying epileptogenic focal cortical dysplasia

Focal cortical dysplasia type II (FCDII) is a malformation of cortical development caused by somatic mutations in the mTOR signaling pathway. Two hallmark pathological cell types in FCDII, dysmorphic neurons (DNs) and balloon cells (BCs), arise as a result of somatic mutations in the mTOR signaling pathway and are implicated in the pathophysiology of drug-resistant epilepsy. However, how these somatic mutations reshape cell states within the human cortex remains poorly understood. Here, we integrate imaging-based spatial transcriptomics (iST), single-nucleus RNA sequencing, and proteomics of surgically resected FCDIIb tissue to define the transcriptional and proteomic profiles of DNs and BCs. Spatial mapping of iST data resolved transcriptional signatures in histologically validated DNs and BCs within FCDIIb sections. Integrative omics analysis further revealed that DNs show upregulation of PI3K-AKT-mTOR and p53-CROT metabolic programs accompanied by suppression of synaptic signaling, whereas BCs exhibit transcriptional signatures of reactive astrocytes with increased phagocytic and immune-like activity. These data delineate cell-type-specific consequences of somatic mTOR pathway mutations at single-cell resolution and reveal previously unrecognized metabolic and immunoregulatory mechanisms contributing to epileptogenesis in drug-resistant epilepsy. Our study establishes a spatial multi-omics framework for dissecting human cortical malformations and highlights potential therapeutic targets for drug-resistant epilepsy.

neuroscience↗

bioRxiv2025

Lineage Analysis and Molecular Characterization of Bergmann Glia-like Progenitors in the Postnatal Mouse Cerebellum using in vivo Electroporation and Spatial Transcriptomics

In the mammalian cerebellum, three types of astroglial cells--Bergmann glial cells (BGs), inner granule cell layer (IGL) astrocytes, and white matter (WM) astrocytes--arise in postnatal timing from two types of progenitors: Bergmann glia-like progenitors (BGLPs) and astrocyte-like progenitors (AsLPs). In contrast to AsLPs, which are commonly observed in other brain regions, BGLPs have not been well studied. Here we investigate their dynamic changes in number, their differentiation abilities and their gene expression profiles during cerebellar development. BGLPs and AsLPs decrease in number as development progresses from P0, and are almost absent by P10. We developed an electroporation-based method to investigate the progeny cells of BGLPs. We found that BGLPs at P6 differentiate into BGs and IGL astrocytes, but not into WM astrocytes, which is consistent with a previous report. However, BGLPs at P0 were observed to differentiate into not only BGs and IGL astrocytes, but also WM astrocytes, indicating that P0 BGLPs possess wider pluripotency than P6 BGLPs. By conducting spatial transcriptomic analysis of the cerebellum at P0 and P6 with over 5,000 probes (Xenium, 5k), we successfully obtained clusters corresponding to BGLPs at P0 and P6, respectively. Further informatics analyses suggested that P0 BGLPs exhibit more stem cell-like features, while P6 BGLPs show a shift toward BG-like characteristics. This study, which includes transcriptome big data, will contribute to understanding the differentiation of BGs and astrocytes, as well as other types of cells, during postnatal cerebellar development.

developmental biology↗

bioRxiv2022

Loss of the MLL3 tumor suppressor accelerates breast tumor onset via HIF1a-induced CCL2-mediated recruitment of CCR2+ regulatory T cells

While essential gatekeepers of immune homeostasis, Foxp3+ regulatory T (Treg) cells infiltrating tumors acquire distinct phenotypes and become highly immunosuppressive, promoting tumor immune escape and growth. How this occurs and relates to tumor-driver mutations is largely uncharacterized. Herein, we created a mouse mammary stem cell-based tumor model using CRISPR gene editing in which we introduced known human cancer-driver mutations. These included functional loss of the MLL3 histone methyltransferase and p53, and constitutive PI3-kinase activation, recapitulating the genetic makeup of aggressive breast cancers. We show that MLL3 loss fosters tumorigenesis by promoting the rapid establishment of an immunosuppressive microenvironment through induction of HIF1, which increases the secretion of the chemokine CCL2 by tumor cells and the recruitment of higher numbers of Foxp3+ Treg cells via CCR2. Greater infiltration of Treg cells also correlates with MLL3 downregulation and mutations in human breast cancer biopsies. Interestingly, HIF1 enforces the differentiation of tumor-infiltrating Treg cells into highly immunosuppressive ICOShiGITRhi Blimp-1hi effector Treg cells that enable rapid tumor escape. Monoclonal antibody targeting of ICOS or GITR inhibits tumorigenesis in most mice even two months after the cessation of treatment as well as the growth of established tumors, suggesting possible therapeutic opportunities for MLL3-mutant breast cancers.

immunology↗

bioRxiv2022

Environmental pH signals the release of monosaccharides from cell wall in coral symbiotic alga

Reef-building corals thrive in oligotrophic environments due to their possession of endosymbiotic algae. Confined to the low pH interior of the symbiosome within the cell, the algal symbiont provides the coral host with photosynthetically fixed carbon. However, it remains unknown how carbon is released from the algal symbiont for uptake by the host. Here we show, using cultured symbiotic dinoflagellate, Breviolum sp., that decreases in pH directly accelerates the release of monosaccharides, i.e., glucose and galactose, into the ambient environment. Under low pH conditions, the cell surface structures were deformed and genes related to cellulase were significantly upregulated in Breviolum. Importantly, the release of monosaccharides was suppressed by the cellulase inhibitor, glucopyranoside, linking the release of carbon to degradation of the agal cell wall. Our results suggest that the low pH signals the cellulase-mediated release of monosaccharides from the algal cell wall as an environmental response in coral reef ecosystems.

evolutionary biology↗

bioRxiv2019

Lateral organ diversification in plants mediated by the ALOG protein family of transcription factors

Land plant shoot structures evolved a diversity of lateral organs as morphological adaptations to the terrestrial environment, in which lateral organs independently evolved in each lineage in the sporophyte or gametophyte generation. The gametophyte meristem of the basally-diverging plant Marchantia polymorpha produces axes with non-photosynthetic scale-like lateral organs instead of leaves. Here we report that an ALOG (Arabidopsis LSH1 and Oryza G1) family protein in Marchantia, MpTAWAWA1 (MpTAW1), regulates meristem maintenance and lateral organ development. A mutation in MpTAW1, preferentially expressed in lateral organs, induces lateral organs with mis-specified identity and increased cell number, and furthermore, causes defects in apical meristem maintenance. Remarkably, MpTAW1 expression rescued the elongated-spikelet phenotype of a rice mutant of MpTAW1 homologue. This suggests that ALOG genes are co-opted to specify lateral organ identities in both gametophyte and sporophyte shoots by repressing lateral organ growth. We propose that the recruitment of ALOG-mediated lateral organ modification was in part responsible for the convergent evolution of independently-evolved lateral organs among highly divergent plant lineages and contributed to the morphological diversification of land plants.

plant biology↗