Biology subjects

Nagaharu, K.

Publications and source records attributed to Nagaharu, K..

4 recordsLinked to original sources

bioRxiv2025

Chromatin Accessibility Shapes Developmental-Specific Lineage Plasticity in Hematopoiesis

Cell differentiation is governed by dynamic changes in chromatin accessibility, and its dysregulation underlies multiple disease states. Prior to birth, development of the hematopoietic system constitutes a period of broad differentiation potential, with certain immune cells arising exclusively during ontogeny. While age is known to affect lineage bias, the underlying molecular differences driving lineage preference in fetal and adult human hematopoietic stem and progenitor cells (HSPCs) remain unclear. Through single-cell cultures of hematopoietic stem cells (HSCs), we observed that fetal cells frequently generate mixed-lineage colonies, whereas adult HSCs are largely restricted to myeloid output. To investigate how these lineage preferences were encoded at the chromatin level, we performed single-cell ATAC-sequencing on first-trimester HSPCs. While adult HSCs showed enrichment of lineage-specific transcription factor motifs, fetal cells lacked such enrichment, consistent with their broader differentiation potential. We additionally uncovered a developmental-specific plasticity in fetal lymphoid progenitors, manifested as a hybrid lympho-myeloid chromatin program not present in adult progenitors. Additionally, the motif for PAX5, master regulator of B cell development, showed markedly reduced accessibility in fetal cells, indicating a more plastic and less committed lymphoid state. This enhanced embryonic lineage plasticity may underlie the prenatal susceptibility to mutational drivers of acute lymphoblastic leukemia.

developmental biology↗

bioRxiv2025

VEGF-C-mediated Cardiac Lymphangiogenesis Promotes Inflammation Resolution in Autoimmune Acute Myocarditis in Mice

BACKGROUNDAcute myocarditis is an immune-mediated inflammatory disease characterized by myocardial inflammation and edema. Cardiac lymphatic vessels are essential for fluid clearance and immune regulation; however, their role in modulating inflammation in autoimmune myocarditis remains largely unclear. METHODSWe investigated the impact of cardiac lymphangiogenesis using a murine model of experimental autoimmune myocarditis induced by cardiac myosin peptide immunization. Human autopsy samples were analyzed for lymphatic expansion. Mice were treated with VEGF-C C156S, a VEGFR3-specific agonist, beginning one week after immunization. Cardiac lymphangiogenesis, myocardial edema, inflammatory infiltration, fibrosis, and cardiac function were evaluated by immunohistochemistry, echocardiography, gene expression analysis, and water content measurements. RESULTSThe VEGF-C treatment accelerated cardiac lymphangiogenesis, enhanced lymphatic drainage, reduced myocardial edema, and attenuated inflammatory cell infiltration and fibrosis. Echocardiography showed the preservation of left ventricular function. VEGF-C selectively decreased the accumulation of iNOS inflammatory macrophages without broadly suppressing T cells or reparative macrophages. Bulk RNA sequencing confirmed the down-regulation of inflammatory gene signatures associated with macrophage activation. CONCLUSIONSThe early stimulation of cardiac lymphangiogenesis by VEGF-C promotes the resolution of inflammation, reduces myocardial injury, and preserves cardiac function in autoimmune myocarditis. Targeting the cardiac lymphatic system may represent a promising therapeutic strategy for acute myocarditis.

pathology↗

bioRxiv2024

Embryological cellular origins and hypoxia-mediated mechanisms in PIK3CA-Driven refractory vascular malformations

Congenital vascular malformations, affecting 0.5% of the population, often occur in the head and neck, complicating treatment due to the critical functions in these regions. Our previous research identified distinct developmental origins for blood and lymphatic vessels in these areas, tracing them to the cardiopharyngeal mesoderm (CPM), which contributes to the development of the head, neck, and cardiovascular system in both mouse and human embryos. In this study, we investigated the pathogenesis of these malformations by expressing Pik3caH1047R in the CPM. Mice expressing Pik3caH1047R in the CPM developed vascular abnormalities restricted to the head and neck. Single-cell RNA sequencing revealed that Pik3caH1047R upregulates Vegf-a expression in endothelial cells through HIF-mediated hypoxia signaling. Human samples supported these findings, showing elevated HIF-1 and VEGF-A in malformed vessels. Notably, inhibition of HIF-1 and VEGF-A in the mouse model significantly reduced abnormal vasculature. These results highlight the role of embryonic origins and hypoxia-driven mechanisms in vascular malformations, providing a foundation for the development of therapies targeting these difficult-to-treat conditions.

molecular biology↗

bioRxiv2024

Inferring extrinsic factor-dependent single-cell transcriptome dynamics using a deep generative model

1RNA velocity estimation helps elucidate temporal changes in the single-cell transcriptome. However, current methodologies for inferring single-cell transcriptome dynamics ignore extrinsic factors, such as experimental conditions and neighboring cell. Here, we propose ExDyn--a deep generative model integrated with splicing kinetics for estimating cell state dynamics dependent on extrinsic factors. ExDyn enables the counterfactual inference of cell state dynamics under different conditions. Among the extrinsic factors, ExDyn can extract key features which have large effects on cell state dynamics. ExDyn correctly estimated the difference in dynamics between two conditions and showed better accuracy over existing RNA velocity methods. ExDyn were utilized for unveiling the effect of PERK-knockout on neurosphere differentiation, hematopoietic stem cell differentiation driven by chromatin activity and the dynamics of squamous cell carcinoma cells dependent on colocalized neighboring cells. These results demonstrated that ExDyn is useful for analyzing key features in the dynamic generation of heterogeneous cell populations.

bioinformatics↗