Biology subjects

Nangaku, M.

Publications and source records attributed to Nangaku, M..

6 recordsLinked to original sources

bioRxiv2026

REN-former prioritizes candidate regulators of kidney disease-state transitions through single-cell foundation modeling and human genetics

Background Acute kidney injury (AKI)-to-chronic kidney disease (CKD) transition is associated with dynamic changes in tubular cell state. However, conventional single-cell transcriptomic analyses primarily identify genes differentially expressed between disease states and do not directly evaluate genes associated with directional transitions between cellular states. Methods We developed REN-former by fine-tuning Geneformer using the GSE183276 single-cell RNA-sequencing dataset from 45 participants representing Normal Reference, AKI, and CKD states. In silico gene deletion and overexpression analyses were used to estimate directional transcriptomic shifts, with a focus on proximal tubular cells. Selected genes were evaluated using summary-data-based Mendelian randomization (SMR), colocalization and expression analysis in additional KPMP participants not included in GSE183276. Results REN-former achieved recall values of 0.99, 0.80, and 0.79 for Normal Reference, AKI, and CKD, respectively. In silico perturbation analyses identified distinct gene programs associated with transitions from Normal Reference to AKI, from Normal Reference to CKD, from AKI to CKD, and from CKD to Normal Reference. Conventional analysis showed metabolic suppression and increased inflammatory and stress-response activation. SMR identified IFITM3, CALR, TTR, CALM1, MUC13, and RPL13, and colocalization supported IFITM3, CALR, TTR, and CALM1. In additional KPMP data, IFITM3 was higher, whereas TTR and CALM1 were lower, in CKD proximal tubules; CALR did not differ significantly. The observed expression changes were concordant with the REN-former-predicted directions for TTR and CALM1 but discordant for IFITM3. Conclusion REN-former provides a framework for prioritizing candidate regulators of kidney disease-associated cell states by integrating predicted perturbation effects with human genetic and transcriptomic evidence.

bioinformatics↗

bioRxiv2026

Open Digital Bioassays Enabled by Aqueous Two-Phase Microreactor Arrays

Digital bioassays enable precise single-molecule quantification but are difficult to adapt to point-of-care testing (POCT) because conventional protocols include off-chip complex processes for sample treatment and sealing, requiring hardware and workflow complexity. We present OASSIS (Open Aqueous two-phase Separation System for Integrated Single- molecule digital bioassay platform), an oil-free and open ATPS platform that localizes both targets and signals in femtoliter-scale dextran (DEX) droplets beneath a polyethylene glycol (PEG) phase. We integrated a CRISPR-Cas13a assay system with a novel, branched fluorescent reporter conjugated to a dextran-binding domain (DBD), which ensures signal retention within the DEX droplets after cleavage. Fluorescence recovery after photobleaching experiments confirmed this robust signal confinement. OASSIS not only performs amplification-free digital RNA detection but also enables serial sample introductions through its open-format architecture that progressively improve sensitivity: the limit of detection (LOD) improved from 1.08 fM (first introduction) to 0.34 fM (third introduction). Furthermore, OASSIS demonstrated specific detection and [~]10-fold enrichment from a complex, denaturant-treated nasopharyngeal swab matrix. Together, these results demonstrate that the open-format architecture of OASSIS provides a practical route toward sensitive, low-complexity POCT and clinical diagnostic applications.

biophysics↗

bioRxiv2026

Applying Spatial Statistics to Spatial Transcriptomics Reveals Local Association Between M2-like Macrophages and Fibrosis in Diabetic Kidney Disease

Renal fibrosis is the common final pathway of chronic kidney disease (CKD), driven in part by myofibroblast-mediated extracellular matrix deposition. M2 macrophages, hereafter referred to as MAC-M2, have been implicated in renal fibrosis, yet whether M2 macrophages are pro- or anti-fibrotic remains controversial, and the spatial context in which MAC-M2-fibrosis coupling occurs is unknown. Here, we applied geographically weighted regression (GWR), a spatial statistical method, to Visium spatial transcriptomics data from diabetic kidney disease (DKD) to characterize spatially resolved high-coupling spots where MAC-M2-fibrosis coupling is significantly positive. In a small DKD cohort (n=6), GWR identified high-coupling spots enriched for B cell and tertiary lymphoid structure (TLS)-like immune signatures, suggesting that the GWR-defined regions captured biologically meaningful immune microenvironments. To gain statistical power for differential gene expression (DEG) analysis, we then applied the same pipeline to the larger Kidney Precision Medicine Project (KPMP) DKD cohort (n=30), in which high-coupling spots showed upregulation of IgE-related immune genes (IGHE, FCER1A) together with the mast cell tryptase TPSB2. These findings suggest that IgE-related immune responses may be present within DKD fibrotic microenvironments characterized by local MAC-M2-fibrosis coupling. As a disease comparison, we further applied the pipeline to a KPMP hypertensive kidney disease (HKD) cohort (n = 27), where high-coupling spot signatures were distinct from DKD and did not show enrichment of IgE-related genes. Together, this study provides the first application of GWR to kidney spatial transcriptomics and suggests that IgE-related immune responses may be a feature of DKD fibrotic microenvironments in which M2 macrophages are locally associated with fibrosis. HighlightsO_LIGeographically weighted regression (GWR) maps spatially variable M2 macrophage-fibrosis coupling in diabetic kidney disease (DKD). C_LIO_LIGWR-defined high-coupling spots show immune activation and loss of kidney-specific programs. C_LIO_LIThe GWR-based analysis was replicated across two independent DKD cohorts. C_LIO_LIIGHE, FCER1A, and the mast cell marker TPSB2 are enriched in high-coupling spots in the KPMP DKD cohort. C_LI

bioinformatics↗

bioRxiv2024

Calcineurin inhibition deactivates pyruvate dehydrogenase and induces proximal tubule cell metabolic dysfunction, causing profibrotic phenotype

Calcineurin inhibitors (CNIs) are indispensable immunosuppressants for transplant recipients and patients with autoimmune diseases, but chronic use causes nephrotoxicity, including kidney fibrosis. Why inhibiting calcineurin, a serine/threonine phosphatase, causes kidney fibrosis remains unknown. We performed single-nucleus RNA sequencing of the kidney from a chronic CNI nephrotoxicity mouse model and found an increased proportion of injured proximal tubule cells, which exhibited altered expression of genes associated with oxidative phosphorylation, cellular senescence and fibrosis. In cultured primary human renal proximal tubule epithelial cells, CNIs caused phosphorylation (deactivation) of pyruvate dehydrogenase, impaired mitochondrial metabolism and senescence-associated phenotypes, all of which were ameliorated by pyruvate dehydrogenase activation. Finally, administration of dichloroacetic acid, a known activator of pyruvate dehydrogenase, in the chronic CNI nephrotoxicity mouse model mitigated kidney fibrosis and the associated transcriptional changes. Collectively, calcineurin inhibition deactivates pyruvate dehydrogenase and induces proximal tubule cell metabolic dysfunction, causing profibrotic phenotype.

molecular biology↗

bioRxiv2021

Oxidized alkyl phospholipids stimulate sodium transport in proximal tubules via PPAR-dependent pathway

The pleiotropic effects of oxidized phospholipids (oxPLs) have been identified. 1-O-hexadecyl-2-azelaoyl-sn-glycero-3-phosphocholine (azPC), an oxPL formed from alkyl phosphatidylcholines, is a potent peroxisome proliferator-activated receptor {gamma} (PPAR{gamma}) agonist. Although it has been reported that thiazolidinediones can induce volume expansion by enhancing renal sodium and water retention, the role of azPC, an endogenous PPAR{gamma} agonist, in renal transport functions is unknown. In the present study, we investigated the effect of azPC on renal proximal tubule (PT) transport using isolated PTs and kidney cortex tissues. We showed that azPC rapidly stimulated Na+/HCO3- cotransporter 1 activity and luminal Na+/H+ exchanger (NHE) activities in a dose-dependent manner, at submicromolar concentrations, in isolated PTs from rats and humans. Additionally, the stimulatory effects were completely blocked by a specific PPAR{gamma} antagonist, 2-chloro-5-nitro-N-phenylbenzamide (GW9662), and a mitogen-activated protein/extracellular signal-regulated kinase (MEK) inhibitor, PD98059. Treatment with an siRNA against PPAR{gamma} significantly suppressed the expression of PPAR{gamma} mRNA, and it completely blocked the stimulation of both Na+/HCO3- cotransporter 1 and NHE activities by azPC. Moreover, azPC induced extracellular signal-regulated kinase (ERK) phosphorylation in rat and human kidney cortex tissues, and the induced ERK phosphorylation by azPC was completely suppressed by GW9662 and PD98059. These results suggest that azPC stimulates renal PT sodium-coupled bicarbonate transport via the PPAR{gamma}/MEK/ERK pathway. The stimulatory effects of azPC on PT transport may be partially involved in the development of volume expansion.

physiology↗

bioRxiv2019

Lysine demethylase 7a regulates the anterior-posterior development in mouse by modulating the transcription of Hox gene cluster

Temporal and spatial colinear expression of the Hox genes determines the specification of positional identities during vertebrate development. Post-translational modifications of histones contribute to transcriptional regulation. Lysine demethylase 7A (Kdm7a) demethylates lysine 9 di-methylation of histone H3 (H3K9me2) and participates in the transcriptional activation of developmental genes. However, the role of Kdm7a during mouse embryonic development remains to be elucidated. Here, we show that Kdm7a-/- mouse exhibits an anterior homeotic transformation of the axial skeleton, including an increased number of presacral elements. Importantly, posterior Hox genes (caudally from Hox9) are specifically downregulated in the Kdm7a-/- embryo, which correlates with increased levels of H3K9me2. These observations suggest that Kdm7a controls the transcription of posterior Hox genes, likely via its demethylating activity, and thereby regulating the murine anterior-posterior development. Such epigenetic regulatory mechanisms may be harnessed for the proper control of coordinate body patterning in vertebrates.

molecular biology↗