Biology subjects

Yagita, K.

Publications and source records attributed to Yagita, K..

6 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

Cryptochrome Loss Drives COPD-like Lung Pathology through Disrupted Alveolar Epithelial Proliferation and Immune Homeostasis

Chronic obstructive pulmonary disease (COPD) is a progressive lung disease characterized by alveolar destruction, impaired epithelial regeneration and chronic inflammation. While circadian disruption has been linked to COPD pathogenesis, the cellular mechanisms remain unclear. Here, we identify the core clock components Cryptochrome 1 and 2 (Cry1/2) as essential regulators of alveolar epithelial cell proliferation and pulmonary immune homeostasis. Cry1/2 double knockout (dKO) mice exhibit spontaneous emphysema-like pathology, including airspace enlargement, increased lung compliance, and inflammatory cell infiltration without environmental insults. Mechanistically, Cry1/2-deficient alveolar epithelial cells display reduced proliferative capacity, and transcriptomic profiling revealed a pronounced shift toward a more proximal airway-like phenotype. Notably, these cells share a gene signature with human COPD lungs in pathways involving immune regulation. Furthermore, Cry1/2-deficient macrophages show elevated responsiveness to LPS. Bone marrow (BM) transplantation revealed that mice receiving Cry1/2 dKO BM suffer from enhanced lung inflammation without airspace enlargement, supporting a critical role of epithelial Cry1/2 in maintaining alveolar integrity. Importantly, treatment with Nobiletin, a circadian rhythm-modulating compound, mitigates NF-{kappa}B activation and ameliorates lung inflammation and structural damage in Cry1/2 dKO mice. These findings establish CRY1/2 as critical circadian regulators of epithelial cell proliferation and immune homeostasis, and highlight the therapeutic potential of targeting circadian pathways in COPD.

genetics↗

bioRxiv2026

11β-HSD2 buffers fetal glucocorticoid exposure inducing Per1 expression under maternal stress

Glucocorticoids (GCs) have been proposed as maternal-fetal communication signals. However, fetal circadian rhythms are initially shielded from maternal entrainment, in addition to delayed circadian clock emergence due to CLOCK suppression. Premature CLOCK/BMAL1 activation disrupts Hes7-driven somite-like structure in gastruloids. Given the genomic proximity of Per1 to Hes7 and their transcriptional ripple effect, the physiological significance of delayed cell-autonomous circadian clock development and the temporal program of maternal-fetal communication during the developmental process have remained unclear. Here, based on a marked decline in Hsd11b2, encoding a GC-inactivating 11{beta}-HSD2 enzyme, during organogenesis, we performed split-litter embryo-transfer experiments in which Hsd11b2 knockout (KO) and wild-type (WT) embryos shared the same maternal environment. Amniotic fluid (AF) GCs remained low and arrhythmic under basal conditions. In contrast, maternal stress caused a pronounced GC surge and Per1 induction in KO, suggesting that 11{beta}-HSD2 buffers acute maternal GC surges. Despite the genomic proximity of Per1 to Hes7 and their transcriptional ripple effect, stress-associated and pharmacological GC exposure recapitulated no overt segmentation defects in vivo. Embryonic stem cell-derived gastruloid assays confirmed that neither GC exposure nor Per1 induction arrested Hes7 oscillations, whereas premature CLOCK/BMAL1 activation impaired these processes even in Hes7 KO gastruloid with ectopic rescue, suggesting that interference with the segmentation clock is mediated by premature CLOCK/BMAL1 activation, not by GC-induced Per1 expression. These findings clearly show that maternal GC signals are selectively buffered during early development. In addition, suppression of CLOCK/BMAL1 activity preserves segmentation clock function, indicating delayed circadian clock emergence is actively regulated during embryogenesis. Significance StatementGCs have been proposed as maternal-fetal communication signals. However, initially, circadian clock is not only suppressed but also shielded from maternal entrainment. Premature CLOCK/BMAL1 activation can disrupt Hes7-driven somitogenesis. In a split-litter Hsd11b2-knockout model, AF GCs remained low and arrhythmic basally but surged after maternal stress in KO embryos, inducing Per1. Despite a genomic position effect of Per1-Hes7 and their putative transcriptional coupling, stress-associated or pharmacological GC exposure did not cause segmentation defects in vivo or disrupt Hes7 oscillations in vitro, whereas CLOCK/BMAL1-driven arrest of Hes7 oscillations persisted in gastruloids despite ectopic Hes7 rescue. These findings identify 11{beta}-HSD2 as a developmental buffer and support the physiological importance of the temporal architecture controlling the timing of circadian clock development.

developmental 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↗

bioRxiv2020

CLOCK/BMAL1 interferes with segmentation clock oscillation in mouse embryonic organoids

In mammals, circadian clocks are strictly suppressed during early embryonic stages as well as pluripotent stem cells, by the lack of CLOCK/BMAL1 mediated circadian feedback loops. During ontogenesis, the innate circadian clocks emerge gradually at a late developmental stage, then, with which the circadian temporal order is invested in each cell level throughout a body. Meanwhile, in the early developmental stage, a segmented body plan is essential for an intact developmental process and somitogenesis is controlled by another cell-autonomous oscillator, the segmentation clock, in the posterior presomitic mesoderm (PSM). In the present study, focusing upon the interaction between circadian key components and the segmentation clock, we investigated the effect of the CLOCK/BMAL1 on the segmentation clock Hes7 oscillation, revealing that the expression of functional CLOCK/BMAL1 severely interferes with the ultradian rhythm of segmentation clock in induced PSM and gastruloids. RNA sequencing analysis showed that the premature expression of CLOCK/BMAL1 affects the Hes7 transcription and its regulatory pathways. These results suggest that the suppression of CLOCK/BMAL1-mediated transcriptional regulation during the somitogenesis may be inevitable for intact mammalian development.

developmental biology↗