Biology subjects

Yamamoto, M.

Publications and source records attributed to Yamamoto, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

ibSLS: A Biobank for Democratizing Access to Multi-Omics Data and Biospecimens from Spaceflight Research

During spaceflight, astronauts are exposed to extreme conditions such as microgravity, cosmic radiation, and confinement, which can cause a wide range of health problems. To elucidate the molecular mechanisms underlying these issues and to develop intervention strategies for maintaining physiological homeostasis during space missions, space life science research using mouse models is actively conducted on the International Space Station (ISS). However, because of the high cost and technical complexity of spaceflight experiments, it is critical to maximize the scientific value of each mission by ensuring broad accessibility to both data and biospecimens. To this end, we developed the integrated biobank for Space Life Sciences (ibSLS; https://ibsls.megabank.tohoku.ac.jp), a data-visualization and sample-sharing platform that provides access to transcriptomic and metabolomic datasets generated from JAXAs Mouse Habitat Unit (MHU) missions. The platform features a user-friendly interface, tools for cross-mission analysis, and integration with human multi-omics databases, enabling cross-species comparisons. In addition, ibSLS facilitates biospecimen requests to support downstream research. By promoting open access to spaceflight-derived data and biological resources, ibSLS encourages the participation of researchers from diverse fields in space life science. We believe that ibSLS will make a valuable contribution to both biomedical research on spaceflight-related health issues and the study of diseases on Earth.

bioinformatics↗

bioRxiv2025

Statistical Causal Discovery in Developing and Refining Adverse Outcome Pathway (AOP)

Statistical causal discovery (SCD) has the potential to advance the development and evaluation of Adverse Outcome Pathways (AOPs) by inferring causal relationships directly from data. However, ecotoxicology data often has challenges for SCD applications, such as missing data and violation of SCD algorithm assumptions. As a proof-of-concept, we applied a linear non-Gaussian acyclic model (LiNGAM), a representative SCD method, to three types of ecotoxicology datasets: (1) bivariate dose-response relationships, (2) bivariate response- response relationships, and (3) a multivariate dataset with a known causal structure. Missing data were addressed through multiple imputation followed by causal estimation using DirectLiNGAM, a direct method for estimating LiNGAM. DirectLiNGAM identified correct causal directions with high statistical reliabilities in three of four bivariate dose-response cases, even when assumptions such as linearity and non-Gaussianity were partially violated. In contrast, response-response cases did not yield a single dominant direction, likely due to the limited number of replicates. In the multivariate case, the inferred graphs closely resembled the expert-curated causal graph, achieving high recall (0.50-0.75), despite relatively low precision (0.31-0.40). These results demonstrate the utility of SCD, combined with multiple imputation, in identifying relevant key events, revealing missing links, and refining existing AOP and quantitative AOP (qAOP) models, under realistic ecotoxicological constraints. SynopsisStatistical causal discovery can advance the development of adverse outcome pathways in a data-driven manner, enabling efficient chemical risk assessment. TOC Art O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/672289v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@117bd64org.highwire.dtl.DTLVardef@19318cdorg.highwire.dtl.DTLVardef@414aecorg.highwire.dtl.DTLVardef@9e068e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Mapping single-cell mechanics in the early embryogenesis of Xenopus laevis using atomic force microscopy

During early embryonic development, cells undergo rapid cleavage divisions accompanied by morphological changes driven by mechanical cues. However, the spatiotemporal mechanics of regulative embryonic cells remains poorly understood. Here, we use atomic force microscopy (AFM) to map single-cell stiffness of Xenopus laevis embryos, a model of regulative development, from early cleavage (stage 6) to the onset of gastrulation (stage 11). To ensure stable AFM mapping, vitelline membrane-removed embryos were immobilized in custom grooved agarose wells and gently held using a dulled glass pipette. AFM observations revealed marked mechanical heterogeneity within the animal hemisphere: stiffness in apical cytoplasmic regions, which are defined as the central apical surface excluding cell-cell boundaries, varied among cells, regardless of size, indicating intrinsic variability. Cell-cell boundaries consistently showed high stiffness, suggesting strong adhesion, as commonly observed in epithelial monolayers in vitro. In contrast, in the vegetal hemisphere during gastrulation, cell-cell boundaries exhibited low stiffness, indicative of weaker adhesion. Additionally, micron-scale stiff inclusions were detected in the apical vegetal cytoplasm, with sizes comparable to those of yolk platelets. These findings demonstrate the capability of AFM to probe the microscale mechanical architecture of developing regulative embryos and to uncover regional mechanical asymmetries between the animal and vegetal hemispheres. Such asymmetries may contribute to key morphogenetic processes during early vertebrate development.

biophysics↗

bioRxiv2025

Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency

The Y chromosome harbors few protein-coding genes, and their roles in early human development remain largely unclear. Here, we demonstrate that UTY, a Y-linked homolog of the histone demethylase UTX, plays a critical, demethylase-independent role in maintaining pluripotency in human embryonic stem cells (hESCs). Despite its low expression and weak enzymatic activity, UTY co-occupies active cis-regulatory elements with UTX and promotes the transcription of key pluripotency genes, including NODAL and LEFTY. Integrated genomic analyses of single and double knockout hESCs reveal that UTY and UTX function redundantly to maintain chromatin accessibility and ensure proper recruitment of core transcription factors such as OCT4 and SOX2. The combined loss of UTY and UTX disrupts transcription factor localization, induces widespread gene expression changes, and leads to a collapse of the pluripotent state, without detectable changes in H3K27 methylation. Instead, these defects are associated with impaired recruitment of ATP-dependent chromatin remodelers and reduced histone acetylation, suggesting a demethylase-independent mechanism. Our findings uncover an essential role for the evolutionarily conserved UTY in safeguarding enhancer function and transcription factor occupancy, highlighting Y-linked regulatory mechanisms that are critical for maintaining human pluripotency. Summary statementThis study reveals how UTX and UTY cooperate to maintain stable gene regulation in human stem cells and guide proper developmental programs.

developmental biology↗

bioRxiv2025

Guanylate-Binding Proteins Promote Host Defense Against Leishmania major by Balancing iNOS/Arg-1 in Myeloid Cells

Cutaneous leishmaniasis (CL) is a debilitating neglected tropical disease characterized by lesions that can range from self-healing to permanent disfigurations. A predominant Th1 response, which stimulates IFN-{gamma} production, is crucial for parasite control during self-healing CL. While IFN-{gamma} primarily activates macrophages to produce nitric oxide via inducible nitric oxide synthase (iNOS) leading to parasite control, IFN-{gamma} also activates other downstream pathways involved in cell autonomous immunity. One such pathway is the activation of guanylate binding proteins (GBPs), a class of interferon inducible GTPases. However, the role of GBPs during CL has been minimally explored. Utilizing RNA-Seq we found that Leishmania major infection leads to the upregulation of several GBPs in C57Bl/6 mice. In vitro studies using GBPChr3 knockout (KO), and C57Bl/6 control mice reveal that bone marrow-derived macrophages (BMDMs) from KO mice exhibit higher parasite burdens following IFN-{gamma} treatment, independent of GBP localization to the parasite. Single-cell RNA-Seq identifies macrophages as the primary expressers of GBPs during L. major infection in vivo. In vivo, GBPChr3 KO mice display increased disease severity and parasite load. GBPChr3 KO macrophages and monocytes show elevated ARG-1 and reduced iNOS expression, indicating a shift toward a parasite-permissive environment that supports parasite growth. These findings highlight a critical role for GBPs in immune-mediated control of CL.

immunology↗

bioRxiv2025

Novel Role of Copper Transporter CTR1 and Therapeutic Potential of Copper Chelators in Retinal Ischemia-Reperfusion Injury

BackgroundRetinal ischemia contributes to vision loss in ischemic and diabetic retinopathies through oxidative stress, neurovascular injury, and inflammation. Copper (Cu), while essential, can be toxic in excess and is regulated by Cu transporters such as CTR1. However, the role of CTR1 in ischemic retinopathy remains unclear. Methods and ResultsRetinal ischemia-reperfusion (IR) injury was induced by elevating intraocular pressure to 110 mmHg for 40 minutes in the right eye of Ctr1 heterozygous (Ctr1/-) and wild-type (WT) mice. In WT mice, IR triggered rapid CTR1 upregulation and increased retinal Cu levels (measured by ICP-MS). IR injury caused retinal ganglion cell loss, inner retinal thinning, vascular degeneration, and apoptosis, all of which were significantly attenuated in Ctr1/- mice. Ctr1/- mice also exhibited reduced microglial (Iba1) and glial cells (GFAP) activation and preserved visual function, as assessed by electroretinography. Mechanistically, IR-induced reactive oxygen species (O2-) production (DHE staining), upregulation of NADPH oxidase components (NOX2, p47phox), and NF-{kappa}B activation were markedly suppressed in Ctr1/- mice. Treatment with the Cu chelator tetrathiomolybdate (TTM) similarly reduced retinal thinning, neurovascular damage, apoptosis, gliosis, and oxidative stress after IR injury. ConclusionsCTR1 plays a central role in mediating Cu-dependent oxidative stress, neurovascular degeneration, and inflammation following retinal IR injury. Targeting the CTR1- Cu axis may represent a novel therapeutic strategy for ischemic retinopathy.

cell biology↗

bioRxiv2025

An in vivo fitness gene of Toxoplasma, MIC11, is essential for PLP1-mediated egress from host cells

After invasion and replication, intracellular pathogens must egress from infected host cells. Toxoplasma gondii facilitates this process by permeabilizing host cells by releasing perforin-like protein 1 (PLP1) through induced microneme secretion. However, the precise mechanism of host cell permeabilization remains enigmatic. Here, we identified the secretory microneme protein MIC11 as a key factor for membrane disruption. A CRISPR-based in vivo screen revealed several genes including MIC11 as an essential gene for virulence. Deletion of MIC11 resulted in severe defects in both membrane rupture and egress. Scanning mutagenesis identified functional motifs in MIC11, and mechanistic analyses demonstrated that MIC11 directly associates with PLP1, regulating its activity in membrane disruption. The MIC11 paralogue MIC22 compensated for MIC11 deletion, suggesting a conserved mechanism of egress in the feline-restricted stages of T. gondii. The discovery of MIC11 advances the understanding of how parasites disrupt host cells to facilitate rapid egress and successful dissemination.

microbiology↗

bioRxiv2024

ATP synthesis of Enterococcus hirae V-ATPase driven by sodium motive force

V-ATPases generally function as ion pumps driven by ATP hydrolysis in the cell, but their capability of ATP synthesis remains largely unexplored. Here we show ATP synthesis of Na+-transporting Enterococcus hirae V-ATPase (EhVoV1) driven by electrochemical potential gradient of Na+ across the membrane (sodium motive force, smf). We reconstituted EhVoV1 into liposome and performed a luciferin/luciferase-based assay to analyze ATP synthesis quantitatively. Our result demonstrates that EhVoV1 synthesizes ATP with a rate of 4.7 s-1 under high smf (269.3 mV). The Michaelis constants for ADP (21 {micro}M) and inorganic phosphate (2.1 mM) in ATP synthesis reaction were comparable to those for ATP synthases, suggesting similar substrate affinities among rotary ATPases regardless of their physiological functions. Both components of smf, Na+ concentration gradient across the membrane ({Delta}pNa) and membrane potential ({Delta}{psi}), contributed to ATP synthesis, with {Delta}pNa showing a slightly larger impact. At the equilibrium points where smf and Gibbs free energy of ATP synthesis are balanced, EhVoV1 showed reversible reactions between ATP synthesis and hydrolysis. The obtained Na+/ATP ratio (3.2 {+/-} 0.4) closely matched the value expected from the structural symmetry ratio between EhVo and EhV1 (10/3 = 3.3), indicating tight coupling between ATP synthesis/hydrolysis and Na+ transport. These results reveal inherent functional reversibility of EhVoV1. We propose that physiological function of EhVoV1 in vivo is determined by relatively small smf against large Gibbs free energy of ATP synthesis, in addition to the absence of inhibitory mechanisms of ATP hydrolysis which are known for ATP synthases.

biophysics↗

bioRxiv2024

JG2: an updated version of the Japanese population-specific reference genome

This study presents the construction of JG2, an updated population-specific reference genome for the Japanese population. Utilizing data from three individuals previously employed in the construction of JG1, several methodologies were employed to enhance genomic coverage and assembly quality. Hi-C sequencing technology facilitated phase-aware assembly, generating two haploid assemblies per individual and enabling improved representation of genetic variation. A meta-assembly strategy and a majority decision approach further refined assembly quality by combining the best sequences from multiple assemblies and minimizing the inclusion of rare variants. The resulting JG2 genome comprises chromosome-level sequences, mitochondrial chromosomes, and unplaced scaffolds, offering more comprehensive coverage of the Japanese genome. Comparative analyses with other reference genomes demonstrated the accuracy and representativeness of JG2, highlighting its utility for genetic research involving the Japanese population. Overall, by adopting the phased assembly technique, JG2 represents a significant advancement over the collapsed assembly-based JG1, providing researchers with a more precise and comprehensive resource for understanding the genetic landscape of the Japanese population. The sequences and annotations are available on the jMorp website (https://jmorp.megabank.tohoku.ac.jp/).

genomics↗

bioRxiv2024

Cardiolipin Inhibits the Noncanonical Inflammasome by Preventing LPS Binding to Caspase 4/11 to Mitigate Endotoxemia in Vivo

In Gram-negative bacterial sepsis, excessive caspase 4/11 activation in response to circulating bacterial lipid LPS (endotoxemia) can cause organ damage and mortality. Current inhibitors of caspase 4/11 also block caspase 1 activity and are therefore not appealing clinical candidates for treating Gram-negative sepsis. Here, we identify double-unsaturated 18:2 cardiolipin as a selective inhibitor of caspase 4/11-dependent inflammatory cytokine secretion and pyroptosis, without affecting caspase-1 responses. Cardiolipin targets the CARD domain of caspase 4/11, impeding its interaction with LPS to restrain caspase 4/11 activation, thereby suppressing endotoxemia-induced systemic inflammation in vivo. Thus, we present cardiolipin as a promising candidate for preventing endotoxemia- induced sequelae in sepsis while preserving caspase-1-driven anti-microbial immune responses. By identifying cardiolipin as a specific caspase 4/11 inhibitor, we provide an urgently-needed tool for studying caspase 4/11 functions in inflammatory pathways, and open the way to studies of noncanonical inflammasome regulation by endogenous cardiolipin.

immunology↗

bioRxiv2024

Systemic injection of scopolamine increased the variability of temporal prediction in head-fixed mice.

Several theories propose that interval timing and memory share common cognitive mechanisms. Pharmacological disruption of the cholinergic system using scopolamine, a muscarinic acetylcholine receptor antagonist, is widely used as a model of cognitive impairment. However, its effects on temporal prediction remain poorly understood. Previous timing studies in freely moving animals are difficult to interpret because motor activity may confound measures of interval timing. Here, we investigated the effects of systemic scopolamine administration on temporal prediction in mice using a head-fixed behavioral paradigm. Mice were trained on a fixed-time schedule task using a peak procedure, in which a 10% sucrose solution was delivered every 10 s through a spout positioned within licking distance. After training, mice developed anticipatory licking responses that peaked around the expected reward time, demonstrating temporal prediction of reward delivery. Systemic administration of scopolamine increased the variability of temporal prediction in a dose-dependent manner without altering the mean peak time. Trial-by-trial analysis further revealed that scopolamine reduced the duration of licking bouts while preserving the total number of licks during peak trials, suggesting impaired maintenance of reward-directed licking behavior rather than altered reward consumption. In a separate open-field assay, scopolamine increased spontaneous locomotor activity and reduced fecal output. These findings demonstrate that cholinergic blockade disrupts the precision of temporal prediction and alters behavioral organization in mice. The increased variability in timing behavior following scopolamine administration may reflect impaired regulation of transitions between behavioral states, providing new insights into the role of cholinergic signaling in temporal cognition.

neuroscience↗

bioRxiv2024

Altered Copper Transport in Oxidative Stress-Dependent Brain Endothelial Barrier Dysfunction Associated with Alzheimer's Disease

Oxidative stress and blood-brain barrier (BBB) disruption due to brain endothelial barrier dysfunction contribute to Alzheimers Disease (AD), which is characterized by beta-amyloid (A{beta}) accumulation in senile plaques. Copper (Cu) is implicated in AD pathology and its levels are tightly controlled by several Cu transport proteins. However, their expression and role in AD, particularly in relation to brain endothelial barrier function remains unclear. In this study, we examined the expression of Cu transport proteins in the brains of AD mouse models as well as their involvement in A{beta}42-induced brain endothelial barrier dysfunction. We found that the Cu uptake transporter CTR1 was upregulated, while the Cu exporter ATP7A and/or ATP7B were downregulated in the hippocampus of AD mouse models, and in A{beta}42-treated human brain microvascular endothelial cells (hBMECs). In the 5xFAD AD mouse model, Cu levels (assessed by ICP-MS) were elevated in the hippocampus. Moreover, A{beta}42-induced reactive oxygen species (ROS) production, ROS-dependent loss in barrier function in hBMEC (measured by transendothelial electrical resistance), and tyrosine phosphorylation of VE-cadherin were all inhibited by either a membrane permeable Cu chelator or by knocking down CTR1 expression. These findings suggest that dysregulated expression of Cu transport proteins may lead to intracellular Cu accumulation in the AD brain, and that A{beta}42 promotes ROS-dependent brain endothelial barrier dysfunction and VE-Cadherin phosphorylation in a CTR1-Cu-dependent manner. Our study uncovers the critical role of Cu transport proteins in oxidative stress-related loss of BBB integrity in AD. HighlightsO_LIUpregulation of the Cu importer CTR1 and downregulation of the Cu exporter ATP7A in the hippocampus of AD mouse models C_LIO_LIA{beta}42 increases CTR1 expression while reduces ATP7A and ATP7B levels in human brain microvascular ECs. C_LIO_LIA{beta}42 triggers increased reactive oxygen species (ROS) production in human brain microvascular ECs through a CTR1- and Cu-dependent manner. C_LIO_LIA{beta}42 induces endothelial barrier dysfunction in human brain microvascular ECs through a CTR1-Cu-ROS-pendent manner. C_LI

neuroscience↗

bioRxiv2024

Disruption of ultrasonic vocalization with systemic administration of the non-competitive N-methyl-d-aspartate receptor antagonist MK-801 in adult male mice

Objective: Social behavior and communication, including ultrasonic vocalizations (USVs), are important for survival and reproductive success across species. N-methyl-D-aspartate (NMDA) receptors contribute to the neural mechanisms underlying social behavior, and pharmacological modulation of these receptors can alter both social behavior and USVs in rodents. However, the effects of NMDA receptor blockade on dyadic USVs and social approach during male-female interactions in mice remain incompletely understood. We therefore investigated the effects of systemic administration of MK-801, a noncompetitive NMDA receptor antagonist, on dyadic vocal activity, social approach, locomotor behavior, and excretory outcomes in adult male mice. Methods: Sexually experienced male mice were tested in male-female interaction and same-sex social-preference tasks. Using VocalMat, a machine-learning-based tool, we classified the USVs recorded during male-female interactions into 11 call categories and examined their temporal relationship to the proximity of the male subject to the female stimulus. Results: Administration of MK-801 to the male dose-dependently reduced the total number of USVs recorded from the male-female dyad, with a marked reduction at the highest dose, while leaving the treated male's proximity to the female stimulus unchanged. In the same-sex social-preference task, MK-801 reduced the time spent near the social stimulus at the highest dose, although preference for the social stimulus over the non-social object remained significant under all treatment conditions. MK-801 also increased locomotor activity and reduced fecal output and estimated urine output in the open-field task. These findings demonstrate that systemic NMDA receptor blockade differentially affects dyadic vocal communication, social approach, locomotor activity, and excretory outcomes. Conclusion: Systemic MK-801 administration to the male reduced the number of USVs recorded during male-female interactions and produced distinct effects on social approach, locomotor activity, and excretory outcomes. These findings indicate that NMDA receptor blockade differentially affects multiple behavioral domains, although the mechanisms underlying the reduction in USVs remain to be determined.

pharmacology and toxicology↗

bioRxiv2024

Visualizing Single V-ATPase Rotation Using Janus Nanoparticles

Understanding the function of rotary molecular motors, such as the rotary ATPases, relies on our ability to visualize the single-molecule rotation. Traditional imaging methods often involve tagging those motors with nanoparticles (NPs) and inferring their rotation from translational motion of NPs. Here, we report an approach using "two-faced" Janus NPs to directly image the rotation of single V-ATPase from Enterococcus hirae, an ATP-driven rotary ion pump. By employing a 500-nm silica/gold Janus NP, we exploit its asymmetric optical contrast - silica core with a gold cap on one hemisphere - to achieve precise imaging of the unidirectional counter-clockwise rotation of single V-ATPase motors immobilized on surfaces. Despite the added viscous load from the relatively large Janus NP probe, our approach provides accurate torque measurements of single V-ATPase. This study underscores the advantages of Janus NPs over conventional probes, establishing them as powerful tools for single-molecule analysis of rotary molecular motors.

biophysics↗

bioRxiv2024

Chromosome-scale genome assembly of acerola (Malpighia emarginata DC.)

Acerola (Malpighia emarginata DC.) is a tropical evergreen shrub that produces vitamin C-rich fruits. Increasing fruit nutrition is one of the main targets of acerola breeding programs. Genomic tools have been shown to accelerate plant breeding even in fruiting tree species, which generally have a long life cycle; however, the availability of genomic resources in acerola, so far, has been limited. In this study, as a first step toward developing an efficient breeding technology for acerola, we established a chromosome-scale genome assembly of acerola using high-fidelity long-read sequencing and genetic mapping. The resultant assembly comprises 10 chromosome-scale sequences that span a physical distance of 1,032.5 Mb and contain 35,892 predicted genes. Phylogenetic analysis of genome-wide SNPs in 60 acerola breeding materials revealed three distinct genetic groups. Overall, the genomic resource of acerola developed in this study, including its genome and gene sequences, genetic map, and phylogenetic relationship among breeding materials, will not only be useful for acerola breeding but will also facilitate genomic and genetic studies on acerola and related species.

genomics↗

bioRxiv2024

Monomer-dimer structural comparison in quinol-dependent nitric oxide reductase reveals a functional basis for superior enzymatic activity in the dimer

The leading cause of bacterial meningitis, Neisseria meningitidis, deploys a quinol-dependent nitric oxide reductase (NmqNOR), belonging to the heme-copper oxidase superfamily. By detoxifying NO, an antimicrobial gas produced by hosts immune system, qNOR enables pathogen survival within hosts. Here, we determined cryoEM structures of the less active monomer and highly active dimer of NmqNOR at resolutions of 2.25 and 1.89 [A], respectively, showing the structural elements responsible for effective NO reduction. Helical disorder at the dimer interface, associated with an altered conformation of the critical Glu563 near the heme/non-heme Fe active site, was observed in the monomer. These findings suggest that dimerization stabilizes the active conformation of Glu563 through the structural network between the dimerization site and the active site. Since other members of the heme-copper oxidases exhibit dimerization, the current data on qNOR helps us understand a regulatory mechanism related to the function of heme-copper oxidases upon oligomerization. TeaserCryoEM structures unveil a functional rationale for dimerization in nitric oxide detoxifying enzyme from a pathogen

biochemistry↗

bioRxiv2024

A large pocket structure surrounding the catalytic center in the BCG protein from Mycobacterium tuberculosis

The widespread prevalence of tuberculosis and the need for extensive chemotherapy in its treatment are caused by the ability of tuberculosis (TB) bacteria to enter a dormant state. Therefore, it is crucial to develop effective compounds that can inhibit the growth of TB bacteria in both the active and dormant states. Previous research has identified agelasine D (marine sponge-derived diterpene alkaloid) capable of resisting dormant mycobacteria. Additionally, BCG3185c has been designated as a target mycobacterial protein. In this study, the crystal structure of BCG3185c was determined at a resolution of 1.86 [A]. Analysis of this crystal structure revealed a large pocket toward the catalytic center of BCG3185c, which is potentially adequate for agelasine D binding. Based on the results of the interaction analysis between agelasine D and Bacillus Calmette-Guerin (BCG) proteins, it was inferred that the binding of agelasine D to this large pocket is crucial for suppressing the growth of Mycobacterium tuberculosis.

biochemistry↗

bioRxiv2024

Visualization of intracellular ATP dynamics in the whole kidney under pathophysiological conditions using the kidney slice culture system

ATP depletion plays a central role in the pathogenesis of kidney diseases. Recently, we reported spatiotemporal intracellular ATP dynamics during ischemia reperfusion (IR) using GO-ATeam2 mice systemically expressing an ATP biosensor. However, observation from the kidney surface did not allow visualization of deeper nephrons or accurate evaluation of ATP synthesis pathways. Here we established a novel ATP imaging system using slice culture of GO-ATeam2 mouse kidneys, evaluated ATP synthesis pathway, and analyzed intracellular ATP dynamics using ex vivo IR and cisplatin nephropathy models. We demonstrated that proximal tubules (PTs) were strongly dependent on oxidative phosphorylation (OXPHOS), whereas podocytes relied on both OXPHOS and glycolysis using ATP synthesis inhibitors. We also confirmed that the ex vivo IR model could recapitulate ATP dynamics in vivo; ATP recovery in PTs after reperfusion varied depending on ischemia length, whereas ATP in distal tubules (DTs) recovered well even after long ischemia. After cisplatin administration, ATP levels in PTs decreased first, followed by a decrease in DTs. An organic cation transporter 2 inhibitor suppressed cisplatin uptake in kidney slices, leading to better ATP recovery in PTs, but not in DTs. Finally, we confirmed that a mitochondria protection reagent delayed cisplatin-induced ATP decrease in PTs. This novel system may provide new insights into the energy dynamics and pathogenesis of kidney disease.

molecular biology↗