Biology subjects

Akiyama, T.

Publications and source records attributed to Akiyama, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Growth-driven mechanical buckling as a mechanism of age-related tortuosity in human cerebral arteries

Human cerebral arteries become increasingly, sometimes abnormally, winding with age, but the mechanical basis of this change remains incompletely understood. To examine how arterial bends form and what sets their spacing, we modeled a cerebral artery as a slender elastic vessel supported by surrounding tissue. The distance between its ends remains constant, and the vessel can bend only in a plane tangent to the brain surface. As its natural length increases, axial compression builds until the vessel buckles. Bending partly relieves the compression, and the resulting waves grow in amplitude as elongation continues. Arterial bending stiffness and tissue support determine the wavelength, which is much larger than and proportional to vessel diameter, with comparatively weak dependence on other parameters. Numerical simulations captured a pre-buckling phase, rapid amplification of waves, and slow post-buckling growth during continued elongation. We evaluated these predictions using three-dimensional centerlines of cerebral arteries reconstructed from magnetic resonance angiography in healthy adults. Older age was associated with greater arterial length and excess-length ratio. For arterial waves oriented mostly parallel to the brain surface, wavelength increased with vessel diameter. Both this relationship and the observed wavelength-to-diameter ratio were consistent with model predictions. However, wave amplitude was not significantly associated with age. Overall, the modeling and imaging results support growth-driven buckling and post-buckling deformation under spatial constraint as a plausible mechanical explanation for age-related cerebral arterial tortuosity. This framework links vascular aging to growth-driven instability and pattern formation, with potential applications to diseased arteries beyond the brain.

biophysics↗

bioRxiv2026

Bacteriostatic lethality emerges from turgor-induced physiological stress

With new antibiotic discovery slowing, maximizing the efficacy of existing drugs is crucial. Bacteriostatic antibiotics are regarded as inferior to bactericidal drugs because they are thought to merely arrest growth without inflicting cellular damage and cell death. Contrary to conventional views, we show that bacteriostasis is a physiologically stressed state, which can be exploited to unmask its lethality. Through quantitative measurements and live-cell imaging, we found that translation inhibition by bacteriostatic antibiotics induces intracellular turgor pressure buildup by perturbing physiological balance in E. coli. This pressure manifests as osmotic swelling, leading to lysis in a subset of cells, while surviving cells depend on PBP1-mediated cell-wall repair, which alleviates mechanical strain. This protective mechanism led us to predict, and we experimentally confirmed, that inactivating PBP1 with a {beta}-lactam amplifies the lethality of bacteriostatic drugs, challenging the general assumption of antagonism between bacteriostatic and bactericidal antibiotics. These findings show bacteriostasis as a physiologically unstable state and provide a systems-level framework for its lethality, enabling the rational design of optimized therapies.

microbiology↗

bioRxiv2026

Whole-genome 3D architectural screen reveals modulators of brain DNA structure

Three-dimensional (3D) genome architecture is the foundation of gene regulation, and plays a critical role in normal physiology and disease. However, our understanding of its biochemical determinants has long been limited by technology: imaging-based screens only profile a small number of loci, while sequencing-based studies rarely exceed 100 samples or conditions. Here we present "in-plate chromosome conformation capture" (Plate-C), a high-throughput, cost-effective platform that profiles thousands of whole-genome architectures in a day. Plate-C enabled the first chemical screen for whole-genome structural changes--profiling 2,956 samples from 834 conditions across 5 neuronal and glial types, accompanied by 6,081 single cells using "easy diploid chromosome conformation capture" (Easy Dip-C) and 200,893 single-cell transcriptomes. We discovered that diverse, dose/time-dependent, and cell type/species-specific modes of DNA structural changes can be rapidly induced by manipulating epigenetic (HDAC, BET), metabolic (mTOR), proteostatic (UPR), developmental (GSK3/Wnt, Hedgehog), immune (cGAS/STING), and neurotransmission pathways. To validate our finding in vivo, we demonstrated in newborn mice that HDAC inhibition drives brain-wide genome rewiring within hours, highly correlated with changes in vitro and inducing a latent structural and transcriptional state orthogonal to normal differentiation. By enabling massively parallel profiling of whole-genome structures, Plate-C paves the way for systematic discovery of DNA folding principles to better understand and engineer the human genome in 3D.

genomics↗

bioRxiv2026

A chromatin relay from AIRE to ETS transcription factors sustains peripheral antigen expression in the thymic mimetic cells to ensure central tolerance.

Medullary thymic epithelial cells (mTECs) establish central tolerance by expressing a diverse repertoire of peripheral tissue-specific antigens (TSAs). This diversity is regulated not only by the transcriptional regulator AIRE, but also by lineage-defining factors in tissue-mimetic, AIRE-negative descendants of Aire mTECs (post-Aire mimetic TECs). However, whether and how prior AIRE activity contributes to TSA expression in post-AIRE mimetic TECs remains unclear. Here, we identify the ETS transcription factors, EHF and ELF3, as key regulators that sustain AIRE-primed gene expression in these cells. EHF and ELF3 preferentially bind distal genomic regions which are rendered accessible in advance by AIRE. Combined loss of EHF and ELF3 disrupts expression of AIRE-regulated genes expressed in mimetic TECs, leading to tissue-selective autoimmunity. Our findings reveal a relay mechanism in which AIRE primes chromatin for ETS factors to maintain TSA expression in post-AIRE mimetic TECs, thereby safeguarding self-tolerance.

immunology↗

bioRxiv2025

LPS O-antigen polysaccharide length impacts outer membrane permeability of enteric gram-negative bacteria

The Gram-negative outer membrane (OM) forms the bacterial cell surface and acts as a barrier against antibiotic influx. In enteric species, the OM is covered by lipopolysaccharides (LPS) decorated with varying lengths of O-antigen (O-Ag) polysaccharide that protect bacteria against mammalian host defenses. Studies of lab-adapted Escherichia coli K-12 strains have proven instrumental in unravelling the essential processes of LPS synthesis, transport, and assembly into the OM. However, O-Ag synthesis was inactivated in K-12 strains during their lab adaption, and these cells produce a non-native, truncated LPS form. Surprisingly, we found that re-activating O-Ag synthesis in K-12 permeabilizes the OM to diverse antibiotics, causing susceptibility. The O-Ag that modifies LPS is directly responsible for the compromised OM barrier. Lengthening the O-Ag polysaccharide worsens antibiotic sensitivity; while shortening it, or removing it entirely, improves antibiotic resistance in both E. coli and the human pathogen, Shigella flexneri. Our data show that OM antibiotic barrier integrity is maintaining by a balanced production of long and short LPS forms, and that this balance is dysfunctional in model E. coli K-12 strains. Our findings reveal that long O-Ag polysaccharides are a double-edged sword: while well-recognized as critical for protection against external host assaults, their transport and assembly onto the surface comes at the inherent price of compromising the OM barrier. Hence, LPS production balances between competing needs in host defense and OM integrity. Moreover, we identify an inherent advantage for species that produce O-Ag-lacking lipooligosaccharide (LOS), rather than LPS. IMPORTANCEThe outer membrane (OM) of bacteria like Escherichia coli and Shigella flexneri forms a barrier that protects cells against antibiotics and immune effectors. The surface-exposed leaflet is filled by lipopolysaccharides (LPS) decorated with long "O-antigen" (O-Ag) polysaccharides. The benefit of covering the surface with O-Ag is well-appreciated - these long polysaccharides shield against host assaults. Our study reveals a hidden cost to these long O-Ag polysaccharides: transporting and assembling LPS modified with O-Ag compromises integrity of the OM antibiotic barrier, rendering bacteria vulnerable to antibiotics. Cells must balance O-Ag across two parameters - protection from the host and preserving OM integrity. Our findings also present an inherent benefit to not producing O-Ag, a common feature among diverse bacterial pathogens.

microbiology↗

bioRxiv2025

Chromatin organizer ASCL1 governs gene programs in thymic epithelial cells, defining immunological self

Immunological self-tolerance depends on medullary thymic epithelial cells (mTECs), which express a broad repertoire of self-antigens to support negative selection of autoreactive T cells and the development of regulatory T cells. Although the autoimmune regulator AIRE is essential for this process, additional factors are required to establish the full mTEC gene expression program. Because thymoma is frequently associated with autoimmunity, implicating defective thymic tolerance, we performed single-cell RNA sequencing of TECs from thymoma patients and identified the transcription factor ASCL1 as selectively downregulated in tumor mTECs. Deletion of Ascl1 in mouse TECs resulted in spontaneous autoimmunity without inducing thymic tumorigenesis. Transcriptomic and chromatin accessibility analyses revealed that ASCL1 influences mTEC gene expression programs and is associated with corresponding changes in chromatin accessibility. Genetic interaction analyses further suggested that ASCL1 activity in immature mTECs modulates the AIRE dependency of gene expression in mature mTECs. Together, these findings identify ASCL1 as a key regulator of mTEC function and central tolerance, providing insight into mechanisms that safeguard immune homeostasis and whose disruption may contribute to autoimmune disease.

immunology↗

bioRxiv2025

KIF5A downregulation in spinal muscular atrophy links axonal regeneration defects with ALS

Spinal muscular atrophy (SMA) is a devastating neuromuscular disorder caused by mutations in the Survival Motor Neuron 1 (SMN1) gene, leading to decreased SMN levels and motor neuron dysfunction. SMN-restoring therapies offer clinical benefit, but the downstream molecular consequences of SMN reduction remain incompletely understood. Here, we demonstrate that SMN deficiency results in downregulation of KIF5A in human neurons and in a mouse model of SMA. We provide evidence that reduced SMN levels impair axon regeneration, which is rescued by KIF5A overexpression and that the RNA-binding protein SMN functions to stabilize KIF5A mRNA. These findings provide evidence of a molecular link between SMA and ALS pathophysiology, highlighting KIF5A as a new SMN target. Our findings suggest SMN-independent interventions targeting KIF5A could represent a complementary therapeutic approach for SMA and other motor neuron diseases.

neuroscience↗

bioRxiv2025

Nonsense-mediated decay masks cryptic splicing events caused by TDP-43 loss

In frontotemporal dementia and amyotrophic lateral sclerosis, the RNA-binding protein TDP-43 is lost from the nucleus, leading to cryptic exon inclusion events in dozens of neuronal genes. Here, we show that many cryptic splicing events have been missed by standard RNA-sequencing analyses because they are substrates for nonsense-mediated decay. By inhibiting nonsense-mediated decay in neurons we unmask hundreds of novel cryptic splicing events caused by TDP-43 depletion, providing a new picture to TDP-43 loss of function in neurons.

neuroscience↗

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

TCR repertoire analysis quantifies effect of irradiation to homeostasis of iNKT cell development in the thymus of mice

Thymic T cell development shows homeostasis in which T cell production recovers after temporal impairment by various stressors. Invariant natural killer T (iNKT) cells in the thymus contribute to recovery of thymic development after irradiation owing to their greater tolerance to irradiation compared to conventional thymocytes. However, whether and how iNKT cell development recovers from irradiation remains unknown. Here we show that iNKT cells in the thymus exhibits much slower post-irradiation recovery than conventional thymocytes. We compared T cell receptor (TCR) alpha chain repertoire of the thymus in 42 days after irradiation and quantified the sustained decline in the number of iNKT cells against other thymocytes. We found that fluctuation of V and J genes usage does not correlate with the number iNKT cells suggesting that differentiation process of iNKT cells after TCR gene rearrangement is impaired by irradiation. Mathematical modelling of recovery dynamics of iNKT cells implied that lack of rapid proliferation immediately after irradiation unlike conventional thymocytes contributes to the prolonged reduction of iNKT cell population. These findings may suggest possibility on association between the prolonged reduction of iNKT cells after irradiation and autoimmune diseases caused by irradiation in bone marrow transplantation.

immunology↗

bioRxiv2025

Clonal effects of the Ras oncogene revealed by somatic mutagenesis in a Drosophila cancer model

Somatic mutations of Ras, encoding a small GTPase, are detected in a wide range of human cancers. Tumor genome sequencing further reveals a cancer type-dependent mutational spectrum for the Ras gene, suggesting that tissue- and allele-specific effects underlie tumorigenic activity. Although biochemical studies have characterized the GTPase activity of several Ras variants in vitro, precisely how somatic mutations of the endogenous Ras locus differentially affect tissue growth and homeostasis remain elusive. Here we engineered the endogenous Drosophila Ras locus to create a spectrum of inducible oncogenic alleles and then compared their activities in vivo. In the developing wing primordium, somatic clones carrying the oncogenic mutation Ras G12V exhibited a weak activation of downstream MAPK signaling but did not disrupt tissue architecture. However, cell clones carrying the same Ras G12V allele in the adult midgut exhibited a growth advantage and progressively took over the tissue, resulting in intestinal barrier dysfunction. In contrast, cell clones expressing a distinct allele, Ras Q61H, formed aberrant cysts that disrupted epithelial architecture and triggered local cell death. Conversely, when we induced cell clones carrying Ras Q61H in the midgut, hyper-proliferating mutant cells rapidly expanded to occupy the entire tissue. Surprisingly, this population of rapidly expanding mutant cells was eventually eliminated from the midgut, restoring wild-type cells and normal barrier function. Thus, in the midgut, Ras G12V was ultimately more deleterious than Ras Q61H due to the regression of Ras Q61H mutant cells. These results establish a new model for somatic mutagenesis at the Ras locus and illuminate a mechanistic basis for the tissue-specific effects of oncogenic Ras variants. Further, this study provides direct evidence that allele-dependent clonal dynamics may play a critical role in the tissue-selectivity of Ras oncogenic mutations.

cancer biology↗

bioRxiv2024

ALS-associated RNA binding proteins converge on UNC13A transcription through regulation of REST

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the selective loss of motor neurons. Although multiple pathophysiological mechanisms have been identified, a unified molecular basis for ALS has remained elusive. The ALS-associated RNA binding protein (RBP) TDP-43 has previously been shown to stabilize UNC13A mRNA by preventing cryptic exon inclusion. We here show that three ALS-associated RBPs--MATR3, FUS, and hnRNPA1--regulate UNC13A expression by targeting the silencing transcription factor REST. These three RBPs bind to and downregulate REST mRNA and thereby promote UNC13A transcription. REST overexpression was detected not only in response to the loss of each of these three RBPs in cultured cells but also in motor neurons of individuals with familial or sporadic ALS. The functional convergence of four RBPs on the regulation of UNC13A, a gene essential for synaptic transmission, highlights a pivotal contribution of these proteins to maitainance of synaptic integrity. Our findings thus provide key insight into ALS pathogenesis and a basis for the development of new therapeutic agents.

neuroscience↗

bioRxiv2024

Direct and indirect RANK ligand and CD40 ligand signaling regulate the maintenance of thymic epithelial cell frequency and properties in the adult thymus

Medullary thymic epithelial cells (mTECs) play a crucial role in suppressing the onset of autoimmunity by eliminating autoreactive T cells and promoting the development of regulatory T cells in the thymus. Although mTECs undergo turnover in adults, the molecular mechanisms behind this process remain unclear. This study describes the direct and indirect roles of receptor activator of NF-{kappa}B ligand (RANKL) and CD40 ligand (CD40L) signaling in TECs in the adult thymus. Flow cytometric and single-cell RNA-seq (scRNA-seq) analyses suggest that the depletion of both RANKL and CD40L signaling inhibits mTEC differentiation from CCL21+ mTEC progenitors to transit-amplifying TECs in the adult thymus. Unexpectedly, this depletion also indirectly affects the gene expression of TEC progenitors and cortical TECs. Notably, AP-1 gene expression, which allows further subdivision of TEC progenitors, is upregulated following the depletion of RANKL and CD40L signaling. Overall, our data propose that RANKL and CD40L signaling cooperatively maintain mature mTEC frequency in the adult thymus and sustain the characteristics of TEC progenitors through an indirect mechanism.

immunology↗

bioRxiv2024

Second impact of an acute total body irradiation on thymic epithelial cells

The thymus, a crucial organ for T cell development, undergoes transient involution following exposure to sublethal total body irradiation. The impact of sublethal irradiation on the thymus is reportedly bimodal: thymic involution recurs after the recovery of the thymus from the initial impact of acute sublethal irradiation. While the second impact of acute irradiation has been acknowledged for thymocytes, its influence on thymic epithelial cells (TECs), which are crucial for thymic T cell differentiation and selection, remains to be elucidated. In this study, we aim to elucidate this influence. Mice were subjected to acute sublethal total body irradiation, and TECs were evaluated at three distinct time points: during the initial impact, during the recovery phase post-initial impact, and during the second impact phase. Flow cytometry analysis revealed that during the second impact phase, mTECs were reduced, whereas cTECs remained unaffected. Among mTECs, the subset expressing high levels of the co-stimulatory molecule CD80 (mTEChi) experienced the most pronounced reduction. RNA sequencing analysis of mTEChi cells at early differentiation stages revealed significant alterations in gene expression profiles during the second impact phase. Notably, gene signatures of tuft-like TECs and Aire-expressing TECs were preferentially influenced in these mTEChi subpopulations. These findings suggest that acute total body irradiation disrupts mTEC frequencies and gene expression in a bimodal manner, possibly compromising thymic functions over extended periods.

immunology↗

bioRxiv2024

Establishing a method for the cryopreservation of viable peripheral blood mononuclear cells in the International Space Station

The analysis of cells frozen within the International Space Station (ISS) will provide crucial insights into the impact of the space environment on cellular functions and properties. The objective of this study was to develop a method for cryopreserving blood cells under the specific constraints of the ISS. In a ground experiment, mouse blood was directly mixed with a cryoprotectant and gradually frozen at -80 {degrees}C. Thawing the frozen blood sample resulted in the successful recovery of viable mononuclear cells when using a mixed solution of dimethylsulfoxide and hydroxyethyl starch as a cryoprotectant. Additionally, we developed new freezing cases to minimize storage space utilization within the ISS freezer. Finally, we confirmed the recovery of major mononuclear immune cell subsets from the cryopreserved blood cells through a high dimensional analysis of flow cytometric data using 13 cell surface markers. Consequently, this ground study lays the foundation for the cryopreservation of viable blood cells on the ISS, enabling their analysis upon return to Earth. The application of this method in ISS studies will contribute to understanding the impact of space environments on human cells. Moreover, this method may find application in the cryopreservation of blood cells in situations where research facilities are inadequate.

cell biology↗

bioRxiv2023

A single-cell atlas of transcribed cis-regulatory elements in the human genome

Transcribed cis-regulatory elements (tCREs), such as promoters and enhancers, are fundamental to modulate gene expression and define cell identity. The detailed mapping of tCREs at single-cell resolution is essential for understanding the regulatory mechanisms that govern cellular functions. Prior tCRE catalogs, limited by bulk analysis, have often overlooked cellular heterogeneity. We have constructed a tCRE atlas using single-cell 5-RNA-seq, capturing over 340,000 single-cells from 23 human tissues and annotating more than 175,000 tCREs, substantially enhancing the scope and granularity of existing cis-regulatory element annotations in the human genome. This atlas unveils patterns of gene regulation, revealing connections between broadly expressed promoters and cell type-specific distal tCREs. Assessing trait heritability at single-cell resolution with a novel tCRE module-based approach, we uncovered the nuanced trait-gene regulatory relationships across a continuum of cell populations, offering insights beyond traditional gene-level and bulk-sample analyses. Our study bridges the gap between gene regulation and trait heritability, underscoring the potential of single-cell analysis to elucidate the genetic foundations of complex traits. These insights set the stage for future research to investigate the impact of genetic variations on diseases at the individual level, advancing the understanding of cellular and molecular basis of trait heritability.

genomics↗

bioRxiv2023

Heart generation via blastocyst complementation in Mesp1/2-deficient mice

Heart transplantation is the only curative option available for patients with advanced heart failure. However, donor organ shortage and graft rejection remain critical challenges in heart transplantation. Blastocyst complementation using pluripotent stem cells (PSCs) can be used to generate organs such as the pancreas and kidneys in animal models with abnormalities in essential developmental genes. Nonetheless, whether functional adult hearts can be generated with blastocyst complementation remains unclear, and it is unknown if parenchyma, blood vessels, and stroma can be generated concomitantly from PSCs using blastocyst complementation to avoid graft rejection. Here, we show the generation of functional adult hearts in acardiac Mesp1 and Mesp2 double-knockout (Mesp1/2-DKO) mice via blastocyst complementation using mouse PSCs. Our result shows that the generated hearts were structurally and functionally normal and restored embryonic lethality in Mesp1/2-DKO mice. All four cardiovascular lineages, including cardiomyocytes, vascular endothelial cells, smooth muscle cells, and cardiac fibroblasts, were virtually entirely derived from exogenous PSCs in the myocardium. Exogenous rat PSCs also generated rat-derived xenogeneic hearts in Mesp1/2-DKO mice via interspecies blastocyst complementation. Thus, blastocyst complementation is a viable technique for generating hearts derived from PSCs and may represent significant progress toward generating rejection-free hearts.

cell biology↗

bioRxiv2023

Mitochondrial protein C15ORF48 is a stress-independent inducer of autophagy that regulates oxidative stress and autoimmunity

Autophagy is primarily activated by cellular stress, such as starvation or mitochondrial damage. However, stress-independent autophagy is activated by unknown mechanisms in several cell types, such as thymic epithelial cells (TECs). Here we report that the mitochondrial protein, C15ORF48, is a critical inducer of stress-independent autophagy. Mechanistically, C15ORF48 reduces the mitochondrial membrane potential and lowers intracellular ATP levels, thereby activating AMP-activated protein kinase and its downstream Unc-51-like kinase 1. Interestingly, C15ORF48 induction of autophagy upregulates intracellular glutathione levels, promoting cell survival by reducing oxidative stress. Mice deficient in C15orf48 showed a reduction in stress-independent autophagy in TECs, but not in typical starvation-induced autophagy in skeletal muscles. Moreover, C15orf48-/- mice developed autoimmunity, which is consistent with the fact that the stress-independent autophagy in TECs is crucial for the thymic self-tolerance. These results suggest that C15ORF48 induces stress-independent autophagy, thereby regulating oxidative stress and self-tolerance.

cell biology↗