Biology subjects

Iwamoto, K.

Publications and source records attributed to Iwamoto, K..

13 recordsLinked to original sources

bioRxiv2026

A rapid, sensitive, and quantitative high plex biomarker digital detection platform enabled by Hypercoding

Low-cost, multiplexed, and automated assays are needed to make omic technologies more broadly accessible in clinical, research, and commercial settings. We present Hypercoding, a scalable technology for detection and quantitation of multi-omic targets. Drawing from data reliability methods in the telecommunications field, Hypercoding uses fluorescent signals from hybridization with an error-correcting code to enable detection of high-plexity targets from biological samples, such as human DNA. In the presence of the target, a linear DNA construct is circularized, immobilized, and amplified to enable single-molecule detection of a target via rapid readout cycles within a 96-well plate. We demonstrate capability for >10,000 code plexity and accurate (98.7%) genotyping of 209 pharmacogenomic variants. Furthermore, we show computation of copy number variation with whole chromosome and sub-gene resolution, as well as quantitation of target abundance down to 10 fM sensitivity with a dynamic range of up to 10 logs.

genomics↗

bioRxiv2026

Hepatic Ketogenesis Attenuates Cardiac Hypertrophy via Metabolic Reprogramming

BackgroundHeart failure with preserved ejection fraction (HfpEF) is increasingly recognized as a multisystem disorder linked to the cardiovascular-kidney-metabolic (CKM) syndrome. While the falling heart undergoes metabolic reprogramming, the interorgan crosstalk regulating myocardial substrate preference in HFpEF remains elusive. We aimed to clarify the role of systemic and local ketogenesis in the pathogenesis of cardiac hypertrophy and HFpEF. MethodsA mouse model of HFpEF was employed using a high-fat diet combined with NG-Nitro-L-arginine methyl ester hydrochloride (L-NAME). Cardiac hypertrophy and systemic metabolic profiling including ketogenesis were evaluated. To dissect the role of site-specific ketogenesis, we generated inducible cardiomyocyte-specific (Hmgcs2{Delta}iCM) and hepatocyte-specific (Hmgcs2{Delta}Hep) knockout mice of HMG-CoA synthase 2 (Hmgcs2), deficient in the rate-limiting enzyme for ketogenesis. Cardiomyocyte -specific nuclei were isolated for transcriptomic (RNA-seq) and in vitro assays in H9C2 cells were used to elucidate molecular mechanisms. ResultsThe HFpEF model successfully exhibited diastolic dysfunction, impaired exercise capacity and cardiac hypertrophy with elevated circulating ketone body concentration. Myocardial metabolomics and snRNA-seq identified a profound metabolic shift characterized by the accumulation of long-chain fatty acids and Krebs cycle intermediates, coupled with the transcriptional downregulation of insulin signaling and fatty acid degradation pathways. Although circulating ketone body level was upregulated, Hmgcs2{Delta}iCM mice showed no exacerbation of the HFpEF phenotype. In contrast, Hmgcs2{Delta}Hep mice exhibited significantly aggravated cardiac hypertrophy (HW/TL; Hmgcs2flox: 7.41 {+/-} 0.87: Hmgcs2{Delta}Hep: 8.29 {+/-} 0.73; p = 0.0154). Mechanistically, hepatic ketogenesis was required to maintain circulating beta-hydroxybutyrate (BHB) levels, which directly modulated cardiomyocyte metabolism. BHB acted as a metabolic signal to dampen fatty acid overload and facilitate glucose utilization. ConclusionsOur study identifies a critical "liver-heart axis" where hepatic ketogenesis serves as an essential regulator of myocardial metabolic resilience. Impaired hepatic ketogenesis creates a metabolic mismatch that drives pathological cardiac remodeling. These findings highlight the liver as a therapeutic target within the CKM syndrome framework, suggesting that restoring the hepato-cardiac metabolic bridge may ameliorate HFpEF progression. What is New?O_LIThis study identifies a novel liver-adipose-heart axis that governs myocardial metabolic resilience during the development of heart failure with preserved ejection fraction (HFpEF). C_LIO_LIWe demonstrate that while both the liver and heart upregulate ketogenesis under metabolic stress, only hepatic ketogenesis--and not cardiac-intrinsic ketogenesis--is essential for mitigating pathological cardiac remodeling. C_LIO_LIMechanistically, liver-derived {beta} -hydroxybutyrate acts as a critical C_LIO_LIendocrine signal that dampens fatty acid oxidation and facilitates myocardial glucose utilization. C_LI What Are the Clinical Implications?O_LIOur findings highlight the liver as a central therapeutic target within the cardiovascular-kidney-metabolic (CKM) syndrome framework, where hepatic metabolic failure directly drives cardiac dysfunction. C_LIO_LIRestoring the hepato-cardiac metabolic bridge, through either hepatic-targeted therapies or ketone body supplementation, represents a promising strategy to enhance myocardial metabolic flexibility and ameliorate HfpEF in patients with multi-organ metabolic disorders. C_LI

biochemistry↗

bioRxiv2025

Genome-wide mapping of sex-associated autosomal DNA methylation in major blood cell types

Sex differences shape human physiology and disease risk, yet their autosomal epigenetic basis remains incompletely understood. Using whole genome bisulfite sequencing data from iMETHYL database ([~]100 adults) across three purified blood cell types (CD4 T cells, monocytes, neutrophils), we performed comprehensive mapping of cell-type specific sex-associated DNA methylation. Using genome-wide Z-test and confidence-interval method, we identified thousands of autosomal differentially methylated sites (DMSs), the majority of which were cell type-specific. We found that neutrophils exhibited pronounced female-biased hypermethylation, whereas CD4 T cells and monocytes showed more balanced patterns. DMSs were enriched within gene bodies and annotated to neuronal and adhesion functions, with T-cell activation uniquely associated in CD4 T cells. Transcription factor binding site enrichment indicated hematopoietic regulators, suggesting that sex-associated methylation is tightly linked to early developmental processes within blood lineages. Differentially methylated regions overlapped genome-wide association study loci for lifetime smoking, multiple sclerosis, and psoriasis, indicating convergence between sex-associated epigenetic states and genetic susceptibility. Evolutionary analysis revealed limited conservation but identified a conserved intronic CpG within FIGN. This study provides the first genome-wide, cell type-resolved map of autosomal sex-associated DNA methylation in human blood and establishes a foundation for mechanistic and translational studies in sex-informed biology and medicine. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/682299v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@18524c0org.highwire.dtl.DTLVardef@2fd8cdorg.highwire.dtl.DTLVardef@142b445org.highwire.dtl.DTLVardef@4949be_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

The Role of Syllabic Rhythm in Speech Perception Across Languages

The insertion of silences at regular intervals restores the intelligibility of English utterances that have been accelerated beyond comprehension, as long as the duration of the resulting speech-silence chunks falls within the theta rhythm of natural speech, i.e. the temporal modulation associated to the syllabic rate. We test whether such a rhythmic strategy works in languages rhythmically different from English, a stress-timed language. Thus, we assess whether comprehension of time-compressed Semantically Unpredictable Sentences (SUS) is restored in the syllable-timed language French and the mora-timed language Japanese, when silences re-establishing theta rhythm are inserted. Restoring the theta rhythm also improved intelligibility in French, but not in Japanese, in which best performance was instead achieved at faster rhythms, which suggests that modulation at the rate of a languages basic rhythmic unit plays a key role in understanding speech. In a second experiment, French speakers listened to SUS with speech-silence chunks adapted to the range of the temporal modulations of the delta, gamma, and high gamma rhythms, which correspond to the rate of prosodic phrases, phonemes, and subsegmental features, respectively. Unlike the theta rhythm, we found no restorative effects, providing further evidence for the special status of the theta rhythm in speech comprehension.

neuroscience↗

bioRxiv2023

RasGEFX triggers spontaneous Ras excitation with RasGEFB/M/U for random cell migration

Excitable systems of eukaryotic chemotaxis can generate asymmetric signals of Ras-GTP-enriched domains spontaneously to drive random cell migration without guidance cues. The molecules responsible for the spontaneous signal generation remain elusive. Here, we characterized RasGEFs encoded in Dictyostelium discoideum by the live-cell imaging of the Ras dynamics and hierarchical clustering, finding that RasGEFX triggers symmetry breaking to generate a Ras-GTP-enriched domain and is essential for random migration in combination with RasGEFB/M/U but dispensable for chemotaxis. Among RasGEFs, RasGEFX and RasGEFB co-localize with Ras-GTP on oscillatory waves propagating along the membrane and regulate the temporal periods and spatial sizes, respectively, of the waves and thus the cytoskeletal dynamics differently. RasGEFU localized uniformly on the membrane and regulated cell adhesion. These findings provide mechanistic insights into the internal signal generation that operates independently of external chemotaxis signaling and suggest a coordinated control of the cytoskeletal dynamics by multiple RasGEFs for spontaneous motility.

molecular biology↗

bioRxiv2023

Genetic associations of dimensional autistic phenotypes

Since there is a large variation in the symptoms shown by persons affected with ASD, analyzing genetics data using a case-control design is not straightforward. To avoid the difficult problem of defining heterogeneous groups, we used four different methods to compute a latent representation of a merged set of three psychometric tests. Computing the genetic contribution of each representation using a subset of participants with genetic data, we showed that factor analysis as well as variable autoencoders separates information contained in psychometric tests into genetically distinct phenotypic domains. Using the individual-level loadings of the domains as quantitative phenotypes in genome-wide association studies we detected statistically significant genetic associations in the domain related to insistence on routine, as well as suggestive genetic signals in other domains. We hope that these results can suggest possible domain-specific interventions in the future.

genetics↗

bioRxiv2022

G protein-biased LPAR1 agonism promotes prototypic antidepressant effects

Prototypic antidepressants, such as tricyclic/tetracyclic antidepressants (TCAs), have multiple pharmacological properties and have been considered to be more effective than newer antidepressants, such as selective serotonin reuptake inhibitors (SSRIs), in treating severe depression. However, the molecular mechanisms underlying the high efficacy of TCAs have not been completely understood. Herein, we found that lysophosphatidic acid receptor 1 (LPAR1), a G protein-coupled receptor, mediates the antidepressant effects of amitriptyline, a typical TCA. Amitriptyline directly bound to LPAR1 and activated downstream G protein signaling without affecting {beta}-arrestin signaling, which implied that amitriptyline could act as a G protein-biased agonist of LPAR1. This biased agonism is unique to TCAs and has not been observed in other antidepressants, such as SSRIs. Long-term infusion of mouse hippocampus with 1-oleoyl-2-O-methyl-glycerophosphothionate (OMPT), a potent G protein-biased LPAR1 agonist, induced behavior similar to that induced by antidepressants. In contrast, LPA, a non-biased agonist of LPAR1, induced anxious behavior, indicating that LPAR1 may regulate conflicting emotional behaviors because of the downstream signaling bias. Furthermore, RNA-seq analysis revealed that LPA and OMPT have opposite patterns of gene expression changes in hippocampus. Ingenuity pathway analysis indicated that chronic intrahippocampal administration of OMPT could activate LPAR1 downstream signaling (Rho and MAPK), whereas LPA suppressed LPAR1 signaling. The results reveal the unique antidepressant effects of TCAs and indicate the potential of G protein-biased agonists of LPAR1 as targets for novel antidepressants.

neuroscience↗

bioRxiv2022

Predicting protease networks through human genetics

By utilizing functional genetic variation within the participants of the UK Biobank project for a largescale PheWAS study we attempted to get a better understanding of how the set of human proteases and their endogenous inhibitors are involved in common diseases. Focusing on known human proteases, their inhibitors, and known substrates, we computed their ranked-biased similarity from phenome-wide association results. Putative regulatory networks were constructed from 250 high-scoring pairs of proteases and related genes. This analysis suggested thirteen network modules, five diagnosis-based and eight biomarker-based. Through genetic associations and published literature on module members, the modules could be classified into different disease modalities including cholesterol homeostasis and high blood pressure.

bioinformatics↗

bioRxiv2022

Puf3p facilitates fermentative mitochondrial functions via monosome-enriched nuclear-encoded mitochondrial mRNAs in budding yeast

Yeasts generally grow with a highly glycolytic metabolism and restrain mitochondrial biogenesis except for some Fe/S proteins. Respiratory mitochondrial functions and biosynthesis pathways are well studied, however how cells coordinate basal fermentative mitochondrial functions is not fully understood. We show that a part of nuclear-encoded mitochondrial mRNAs, which preferentially translated in monosomes, are regulated by Puf3p upon glucose-rich media. Especially, of those monosome-enriched nuclear-encoded mitochondrial mRNAs, CAT5/COQ7 mRNA has a variant of the canonical Puf3p binding site on its 3-UTR. Western blot analysis showed that Puf3p represses the translation of Cat5p regardless of fermentable or respiratory media. In vitro binding assay revealed that Puf3p directly binds to CAT5 mRNA via the non-canonical Puf3p binding site. Mutants harboring the substitution of the non-canonical Puf3p binding site in CAT5 mRNA grew normally but impaired Cat5p expressions apparently, indicating CAT5 mRNA is a bona fide Puf3p target. Overall, Puf3p, a general key modulator for nuclear-encoded mitochondrial mRNAs, fine-tunes translation of a subset of nuclear-encoded mitochondrial mRNAs including mRNAs with non-canonical Puf3p binding sites under the fermentation. This may be required to keeping the fundamental functions of yeast mitochondria at proper levels.

molecular biology↗

bioRxiv2021

Transcriptomic analysis of astaxanthin hyper-producing Coelastrum sp. mutant obtained by chemical mutagenesis

A newly isolated green microalga, Coelastrum sp. has the capability to produce and accumulate astaxanthin under various stress conditions. At present, a mutant G1-C1 of Coelastrum sp. obtained through chemical mutagenesis using ethyl methane sulfonate displayed an improvement in astaxanthin accumulation, which was 2-fold higher than that of the wild-type. However, lack of genomic information limits the understanding of the molecular mechanism that leads to a high level of astaxanthin in the mutant G1-C1. In this study, transcriptome sequencing was performed to compare the transcriptome of astaxanthin hyper-producing mutant G1-C1 and wild-type of Coelastrum sp. with respect to astaxanthin biosynthesis. This is to clarify why the mutant produced higher astaxanthin yield compared to the wild-type strain. Based on the transcriptomic analysis, the differentially expressed genes involved in astaxanthin biosynthesis were significantly upregulated in the mutant G1-C1 of Coelastrum sp. Genes coding phytoene synthase, phytoene desaturase,{zeta} -carotene desaturase, and lycopene {beta}-cyclase involved in {beta}-carotene biosynthesis in the mutant cells were upregulated by 10-, 9.2-, 8.4-, and 8.7-fold, respectively. Genes coding beta-carotene ketolase and beta-carotene 3-hydroxylase involved in converting {beta}-carotene into astaxanthin were upregulated by 7.8- and 8.0-fold, respectively. In contrast, the lycopene {varepsilon}-cyclase gene was downregulated by 9.7-fold in mutant G1-C1. Together, these results contribute to higher astaxanthin accumulation in mutant G1-C1. Overall, the data in this study provided molecular insight for a better understanding of the differences in astaxanthin biosynthesis between the wild-type and mutant G1-C1 strains.

molecular biology↗

bioRxiv2020

Inter-breeder differences in prepulse inhibition deficits of C57BL/6J mice in a maternal infection model for schizophrenia

Genetic and environmental factors interact with each other to influence the risk of various psychiatric diseases; however, the intensity and nature of their interactions remain to be elucidated. We used a maternal infection model using polyinosinic-polycytidylic acid (Poly(I:C)) to determine the relationship between the maternal breeding environment and behavioral changes in the offspring. We purchased pregnant C57BL/6J mice from three breeders and administered Poly(I:C) (2 mg/kg) intravenously in their tail vein on gestation day 15. The offspring were raised to 8-12 weeks old and subjected to the acoustic startle tests to measure their startle response intensity, prepulse inhibition levels, and degree of the adaptation of the startle response. No statistical interaction between Poly(I:C) administration and sex was observed for prepulse inhibition; thus, male and female mice were analyzed together. The Poly(I:C) challenge significantly decreased prepulse inhibition levels of the offspring born to the pregnant dams from Breeder A but not those from the other breeders. However, there were no significant inter-breeder differences in Poly(I:C) effects on startle response and on startle adaptation. The rearing environment of mouse dams has a prominent impact on the Poly(I:C)-induced prepulse inhibition deficits in this maternal infection model.

neuroscience↗

bioRxiv2020

Promoter activity-based case-control association study on SLC6A4 highlighting hypermethylation and altered amygdala volume in male patients with schizophrenia

Associations between altered DNA methylation of the serotonin transporter (5-HTT)-encoding gene SLC6A4 and early life adversity, mood and anxiety disorders, and amygdala reactivity have been reported. However, few studies have examined epigenetic alterations of SLC6A4 in schizophrenia (SZ). We examined CpG sites of SLC6A4, whose DNA methylation levels have been reported to be altered in bipolar disorder, using three independent cohorts of patients with SZ and age-matched controls. We found significant hypermethylation of a CpG site in SLC6A4 in male patients with SZ in all three cohorts. We showed that chronic administration of risperidone did not affect the DNA methylation status at this CpG site using common marmosets, and that in vitro DNA methylation at this CpG site diminished the promoter activity of SLC6A4. We then genotyped the 5-HTT-linked polymorphic region (5-HTTLPR) and investigated the relationship among 5-HTTLPR, DNA methylation, and amygdala volume using brain imaging data. We found that patients harboring low-activity 5-HTTLPR alleles showed hypermethylation and they showed a negative correlation between DNA methylation levels and left amygdala volumes. These results suggest that hypermethylation of the CpG site in SLC6A4 is involved in the pathophysiology of SZ, especially in male patients harboring low-activity 5-HTTLPR alleles.

genetics↗

bioRxiv2019

pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems

BackgroundStudies using quantitative experimental methods have shown that intracellular spatial distribution of molecules plays a central role in many cellular systems. Spatially resolved computer simulations can integrate quantitative data from these experiments to construct physically accurate models of the systems. Although computationally expensive, microscopic resolution reaction-diffusion simulators, such as Spatiocyte can directly capture intracellular effects comprising diffusion-limited reactions and volume exclusion from crowded molecules by explicitly representing individual diffusing molecules in space. To alleviate the steep computational cost typically associated with the simulation of large or crowded intracellular compartments, we present a parallelized Spatiocyte method called pSpatiocyte. ResultsThe new high-performance method employs unique parallelization schemes on hexagonal close-packed (HCP) lattice to efficiently exploit the resources of common workstations and large distributed memory parallel computers. We introduce a coordinate system for fast accesses to HCP lattice voxels, a parallelized event scheduler, a parallelized Gillespies direct-method for unimolecular reactions, and a parallelized event for diffusion and bimolecular reaction processes. We verified the correctness of pSpatiocyte reaction and diffusion processes by comparison to theory. To evaluate the performance of pSpatiocyte, we performed a series of parallelized diffusion runs on the RIKEN K computer. In the case of fine lattice discretization with low voxel occupancy, pSpatiocyte exhibited 74% parallel efficiency and achieved a speedup of 7686 times with 663552 cores compared to the runtime with 64 cores. In the weak scaling performance, pSpatiocyte obtained efficiencies of at least 60% with up to 663552 cores. When executing the Michaelis-Menten benchmark model on an eight-core workstation, pSpatiocyte required 45- and 55-fold shorter runtimes than Smoldyn and the parallel version of ReaDDy, respectively. As a high-performance application example, we study the dual phosphorylation-dephosphorylation cycle of the MAPK system, a typical reaction network motif in cell signaling pathways. ConclusionspSpatiocyte demonstrates good accuracies, fast runtimes and a significant performance advantage over well-known microscopic particle simulators for large-scale simulations of intracellular reaction-diffusion systems. The source code of pSpatiocyte is available at https://spatiocyte.org.

systems biology↗