Biology subjects

Matsumoto, A.

Publications and source records attributed to Matsumoto, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Physiological mapping and prediction reveal stress-responsive translation initiation landscapes

Translation initiation defines the protein output of the transcriptome, but its physiological dynamics in cells and tissues remain incompletely characterized. Here we develop TISCA2, an inhibitor-free method that captures eIF5B-associated initiating ribosomes to map translation initiation sites genome-wide. By directly identifying start sites rather than inferring translation from elongating-ribosome periodicity, TISCA2 improves the detection of short and overlapping translons. Translation of a subset of TISCA2-identified translons is supported by N-terminal proteomics and HLA-I immunopeptidomics. The arsenite-induced integrated stress response broadly redistributes start-site usage, reducing upstream initiation in favor of downstream initiation. TISCA2 further reveals tissue-specific initiation landscapes in vivo, with increased detection of downstream candidate start sites in the testis. Finally, we develop IncepTIS, a sequence-based deep learning model that predicts position-resolved and condition-dependent initiation landscapes. IncepTIS-guided optimization generates de novo mRNA 5' leaders with stress-responsive initiation patterns. Together, TISCA2 and IncepTIS provide an experimental and computational framework for mapping, predicting and engineering translation initiation in mammalian cells and tissues.

molecular biology↗

bioRxiv2026

Differential physiological, behavioral, and medial prefrontal cortex transcriptomic responses to chronic restraint stress between BALB/c and C57BL/6J mice

Chronic stress is a major risk factor for psychiatric disorders such as depression and anxiety, yet the biological basis of individual differences in stress susceptibility and resilience remains poorly understood. Here, we examined physiological, behavioral, and medial prefrontal cortex (mPFC) transcriptomic responses to chronic restraint stress (CRS) in male BALB/c and C57BL/6J mice. After 21 days of CRS, BALB/c mice exhibited greater stress-related changes than C57BL/6J mice, including greater body weight loss, elevated serum corticosterone, reduced serum antioxidant capacity, and more pronounced depression-like behaviors. RNA sequencing showed largely strain-specific transcriptional changes in the mPFC. Strain x stress interaction analysis, followed by canonical pathway analysis using Ingenuity Pathway Analysis (IPA), identified strain-dependent molecular signatures. The most prominent differences involved extracellular matrix (ECM) organization and remodeling and neuroinflammatory signaling pathways, with greater predicted activation in BALB/c mice. IPA upstream regulator analysis further predicted multiple candidate regulators associated with these pathways, including TGF-{beta}/SMAD, C4a/C4b, and MAPK14. Among genes associated with these pathways, several ECM-related genes were preferentially upregulated in BALB/c mice, whereas activity-dependent immediate early genes were preferentially downregulated in C57BL/6J mice. These findings suggest that the strain-dependent mPFC transcriptional programs identified here may contribute to differential stress susceptibility and resilience.

neuroscience↗

bioRxiv2026

Ablation of GM3 Gangliosides in cardiomyocytes modestly impacts heart size but does not protect the murine heart against ischemia reperfusion injury

Advances in mass spectrometry have seen the identification of hundreds of new lipid species, some of which have been found to be associated with adverse cardiac remodeling. Key among these are GM3 gangliosides, which have been associated with metabolic disease, and more recently, adverse cardiac remodeling. Whether GM3s have a direct pathophysiological effect in the heart remains unclear. The present study investigated the effects of cardiomyocyte-specific knockout of GM3 synthase (GM3S, enzyme responsible for the synthesis of GM3) in the heart under basal settings and in response to ischemia-reperfusion (I/R) injury. A new cardiomyocyte-specific GM3S knockout (KO) model was generated, with knockout confirmed via lipidomic profiling. Under basal conditions, male GM3SKO mice exhibited reduced heart weight to tibia length (HW/TL) ratios with no evidence of pathological remodeling, while female mice showed no significant morphological differences. Male GM3SKO mice subjected to 1 hour ischemia and 4 weeks reperfusion demonstrated reduced HW/TL ratio compared to control mice subjected to I/R. However, no significant differences were observed in cardiac function, heart failure and fibrotic markers. Lipidomic profiling (49 classes, [~]850 species) revealed significant accumulation of dihexosylceramide, a metabolic precursor of GM3 in the male heart under basal and post-I/R conditions. In male GM3SKO I/R hearts, GM3 reduction was associated with decreases in odd- and branch-chained phospholipids, together with distinct changes in circulating ether lipid species. Collectively, cardiomyocyte-specific GM3 depletion contributed to sphingolipid remodeling but did not confer protection against I/R-mediated injury. These findings suggest that elevated GM3 levels observed in settings of cardiac pathology are not cardiomyocyte driven, highlighting the importance of understanding cell-type specific contributions to adverse cardiac remodeling.

physiology↗

bioRxiv2026

Large-scale dimensional behavioral profiling dissociates fear memory from locomotor confounds in mice: The necessity of baseline-normalized metrics

Fear conditioning is widely used to assess associative memory in mice, yet percent freezing conflates memory with baseline locomotor and anxiety-related traits. A systematic survey of recent studies (2020-2025) found that fewer than 1% statistically integrate locomotor activity into freezing analyses. Here, we address this gap using a large-scale dataset of >10,000 mice across >160 comparisons, including genetic mutations, pharmacological interventions and aging, tested in 15 standardized behavioral paradigms. Conventional freezing scores covaried strongly with general locomotor activity, obscuring memory-related phenotypes. Multiple factor analysis identified two principal behavioral dimensions, locomotor activity and learning/memory: conventional freezing aligned with the locomotor dimension, whereas freezing subtraction and the activity suppression ratio mapped onto the memory dimension and improved detection of synaptic plasticity phenotypes. These analyses show that baseline locomotor normalization is essential for interpreting fear conditioning as a memory assay and provide an open framework for selecting and reporting locomotor-normalized metrics.

neuroscience↗

bioRxiv2026

Distinct optokinetic reflex phenotypes in Frmd7 and Chrnb2 mutant mice

HighlightsBinocular rotational stimulation enhances OKR in wild-type mice along both axes. Chrnb2tm mice show spontaneous horizontal eye oscillations regardless of input. Frmd7tm mice lack binocular enhancement of vertical OKR. The optokinetic reflex (OKR) stabilizes retinal images during global motion and depends on retinal direction-selective (DS) circuits. Although multiple mutant mouse strains exhibit impaired DS circuits via distinct mechanisms, differences in OKR phenotypes remain unexplained. Here, we developed a behavioral system to quantify mouse eye movements under controlled rotational and translational visual stimuli. Using this platform, we examined OKR in wild-type (WT) mice and two DS circuit mutants: Frmd7tm mice, which lack horizontal DS tuning and horizontal OKR, and Chrnb2tm mice, which have disrupted {beta}2-nAChR-dependent cholinergic spontaneous activity during development. Consistent with previous research, both mutants lacked horizontal OKR across conditions, while vertical OKR was preserved. We found that Chrnb2tm mice exhibited spontaneous horizontal eye oscillations regardless of visual input. This phenotype was absent in Frmd7tm mice, suggesting that defective retinal waves in Chrnb2tm mice may induce circuit-level instability distinct from the loss of horizontal DS tuning alone. In addition, WT mice showed enhanced vertical OKR under binocular rotational stimulation, which was absent in Frmd7tm mice. Together, these findings provide a functional comparison of Frmd7tm and Chrnb2tm mice and establish a quantitative framework for dissecting how specific genetic perturbations alter the retinal computations underlying horizontal and vertical OKR.

neuroscience↗

bioRxiv2026

A Knock-In Igfn1iCre transgenic mouse line provides partial developmental access to type-7 bipolar cells

1.Functional neuronal circuits in the vertebrate retina emerge through coordinated developmental events, yet the timeline by which bipolar cells acquire visual feature selectivity remains unclear. A major barrier is the limited genetic access to bipolar subtypes during early postnatal stages. Recent comprehensive transcriptomic study points to Igfn1 as a molecular marker for type-7 bipolar cells (BC 7), a subtype that exhibits direction-selective glutamate releases in adult. Here, we generated an Igfn1iCre knock-in mouse line and characterized Igfn1-positive cell morphology from postnatal day 4(P4) to adult using Cre-dependent tdTomato reporter mice. We found Igfn1-positive cells in the inner retina by P12-P15, predominantly labelling bipolar cells and some amacrine populations. At P15, about 71% of labelled bipolar cells stratified their axons in the S4 sublamina of the inner plexiform layer, consistent with BC 7 morphology. In adult retina, the widespread Igfn1-labelling appears slightly dominated in amacrine cells. To validate these observations, we analysed Igfn1 expression in the Mouse Retina Cell Atlas and confirmed strong Igfn1 enrichment in BC 7 and expression in additional retinal cell types, mirroring experimental results. Overall, these results reveal Igfn1iCre as a potential developmental tool for BC 7 access in the retina.

neuroscience↗

bioRxiv2026

Vitronectin defines a differentiation-restraining extracellular matrix state in myogenic cells

Skeletal muscle differentiation is classically triggered by reducing serum-derived mitogenic cues; however, the extracellular matrix-associated factors that actively maintain a proliferative, differentiation-resistant state remain poorly defined. Here, we identify vitronectin (VN) as a key extracellular matrix gatekeeper that controls myogenic cell fate. VN is abundant in fetal bovine serum but largely absent from horse serum, rapidly declines upon differentiation induction, and selectively suppresses myogenic differentiation while sustaining proliferation through integrin v{beta}3-dependent signaling. VN maintains growth factor receptor activity and cell-cycle progression even under differentiation conditions, thereby preventing myoblast commitment. These effects extend to three-dimensional culture and primary embryonic chicken myogenic cells, indicating evolutionary conservation. Importantly, VN progressively accumulates during long-term passaging, coinciding with replicative senescence and impaired differentiation, and inhibition of v{beta}3 signaling partially restores myogenic competence in senescent cells. Together, our findings redefine a long-standing myoblast culture paradigm by identifying a serum-derived extracellular matrix protein as a decisive regulator linking extracellular environment, proliferative niche maintenance, and age-associated decline in myogenic competence.

cell biology↗

bioRxiv2025

High-Throughput Measurement of Oxidative Stress Indicators: d-ROMs and BAP Assays in a 384-Well Plate Format

The bodys oxidative balance is regulated by systems that produce and eliminate reactive oxygen species (ROS), and disruptions in this balance can contribute to the development of lifestyle-related diseases. d-ROMs and BAP tests, which evaluate oxidative balance using just 30 {micro}L of serum per sample in approximately 10 minutes, are widely used for this purpose. However, these methods are not suitable for large-scale studies due to their low-throughput and cost. To overcome these limitations, we established a simultaneous measurement system for multiple samples (144 samples) for measuring d-ROMs and BAP using a pipetting robot and a 384-well plate. The developed system demonstrated good linearity and reproducibility, while significantly reducing reagent and sample consumption. Measurement differences compared to the one of the currently available FREE Carrio Duo system ranged from -5% to 3% for d-ROMs and -12% to 8% for BAP, indicating high consistency with existing methods. Furthermore, the measurement time was substantially shortened from 24 hours (10 minutes x 144 samples) to at longest four hours, although the final color measurements for d-ROMs were performed one week later. This optimized semi-automated system enables the precise and efficient measurement of oxidative stress markers, making it suitable for large-scale studies.

biochemistry↗

bioRxiv2025

Expanded gene targeting in RNA hacking with G-tract-supply Staple oligomer

RNA hacking (RNAh) is a gene regulation technology that employs a short oligonucleotide, termed a Staple oligomer, to induce the formation of RNA G-quadruplex structures on target mRNAs. While RNAh has the potential to target approximately 65% of human mRNAs, its applicability to the remaining genes is restricted by the sequence constraints. Herein, we present the G-tract-supply Staple oligomer (Gs-Staple oligomer), designed to expand the range of targetable mRNAs within the RNAh framework. Incorporating G-tracts into Staple oligomers alleviates the sequence constraints, enabling access to a broader range of mRNA targets. Gs-Staple oligomers effectively suppressed the translation of target proteins in mammalian cells and in vivo. Furthermore, the gene suppression could be precisely modulated by adjusting the linker length between the G-tracts. These findings have significantly expanded the versatility of RNAh, suggesting its potential for further development while highlighting its potential to be utilized as a nucleic acid-based tool for research and clinical medicine.

bioengineering↗

bioRxiv2025

iGABASnFR2: Improved genetically encoded protein sensors of GABA

Monitoring GABAergic inhibition in the nervous system has been enabled by development of an intensiometric molecular sensor that directly detects GABA. However, the first generation iGABASnFR exhibits low signal-to-noise and suboptimal kinetics, making in vivo experiments challenging. To improve sensor performance, we targeted several sites in the protein for near-saturation mutagenesis and evaluated the resulting sensor variants in a high throughput screening system using evoked synaptic release in primary cultured neurons. This identified a sensor variant, iGABASnFR2, with 4.1-fold improved sensitivity and 30% faster rise time, and binding affinity that remained in a range sensitive to changes in GABA concentration at synapses. We also identified sensors with an inverted response, decreasing fluorescence intensity upon GABA binding. We termed the best such negative-going sensor iGABASnFR2n, which can be used to corroborate observations with the positive-going sensor. These improvements yielded a qualitative enhancement of in vivo performance when compared directly to the original sensor. iGABASnFR2 enabled the first measurements of direction-selective GABA release in the retina. In vivo imaging in somatosensory cortex revealed that iGABASnFR2 can report volume-transmitted GABA release following whisker stimulation. Overall, the improved sensitivity and kinetics of iGABASnFR2 make it a more effective tool for imaging GABAergic transmission in intact neural circuits.

neuroscience↗

bioRxiv2025

Inducible degradation of endogenous proteins by AlissAID system and development of a photoactivatable inducer.

Protein analysis strategies involving targeted protein degradation are powerful approaches to determine gene functions. Auxin-inducible degron (AID) is among the most widely used methods for target protein knockdown. This system enables the rapid depletion of AID-tagged target proteins in an auxin-dependent manner. Various improved AID methods have been developed to date; however, the requirement to tag the target protein remains a common challenge. Here, we demonstrated the efficiency of the affinity-linker-based super-sensitive AID system for condition-knockdown of target proteins in cultured animal cells and mouse embryos. This system combines the improved AID method with small-molecule antibodies, enabling the control of GFP and mCherry fusion proteins. Additionally, this system can be used to degrade endogenous targets, such as Ras proteins. We also developed a novel inducer, caged 5-adamantyl-IAA, that precisely controlled targeted protein degradation under light irradiation. This advanced technique aids in the degradation of endogenous proteins of interest and can be used to develop new technologies for localized protein degradation.

cell biology↗

bioRxiv2024

Chemotherapy resistance due to epithelial-to-mesenchymal transition is caused by abnormal lipid metabolic balance

Invasive cancer is defined by the loss of epithelial cell traits resulting from the ectopic expression of epithelial-mesenchymal transition (EMT)-related transcription factors such as Snail. Although EMT is known to impart chemoresistance to cancer cells, the precise molecular mechanisms remain elusive. We found that Snail expression confers chemoresistance by upregulating the cholesterol efflux pump ABCA1 as a countermeasure to the excess of cytotoxic free cholesterol relative to its major interaction partner in cellular membranes, sphingomyelin. This imbalance is introduced by the transcriptional repression of enzymes involved in the biosynthesis of sphingomyelin by Snail. Inhibiting esterification of cholesterol, which renders it inert, selectively suppresses growth of a xenograft model of Snail-positive kidney cancer. Our findings offer a new perspective on lipid-targeting strategies for invasive cancer therapy.

cell biology↗

bioRxiv2024

Regional differences in cell characteristics in electric eel electric organs indicate electrocyte development with ventral to dorsal migration.

Electric eels (Electrophorus) are renowned for their ability to generate electric discharge, which is used for prey capture and defense. Their electric organs (EOs) are located along the lateral-ventral region of the tail and contain electrocytes, which are multinucleated syncytium cells. The developmental origin of the electrocyte is mesodermal lineage cells observed in the ventral part of the myotome. However, it is unclear whether these precursor cells are also maintained in later stages and contribute to electric organ growth in adulthood. In this study, we report regional differences in cell morphology within the main EO (mEO) and identify a candidate cell population for electrocyte progenitors at the juvenile stages of Electrophorus. The cell morphology and distribution from the ventral terminal to the dorsal region of the mEO suggest the segregation of progenitors from the ventral cluster and their gradual transformation into mature multinucleated electrocytes via cell fusion and layering along the dorsal axis. Immunohistochemistry revealed strong expression of sodium-potassium adenosine triphosphatase (Na+/K+-ATPase), a key component in generating electric discharge in the mEO, across most mEO regions, except in the ventral cluster cells. Based on these observations, we propose that electrocyte progenitors develop from ventral cluster cells in the mEO and differentiate into mature multinucleated cells as they migrate dorsally. This is the first report to approach the developmental process of Electrophorus electrocytes from cell morphology and genetic profiles. Our findings represent a breakthrough in understanding the differentiation of electrocytes during the growth stages of Electrophorus.

developmental biology↗

bioRxiv2024

Exploring 3-Aminobenzoic Acid as a Therapeutic Dietary Component for Enhancing Intestinal Barrier Integrity in Ulcerative Colitis

BackgroundDietary components and their metabolites produced by intestinal bacteria play a crucial role in maintaining intestinal epithelial integrity. Disrupted epithelial integrity increases permeability and leads to chronic inflammation in the colon, known as ulcerative colitis (UC), in genetically predisposed individuals. However, the gut microbial metabolites regulating epithelial permeability remain unexplored and their metabolism in UC patients is unclear. MethodsA library of 119 gut microbial metabolites was screened for their ability to reduce epithelial permeability in Caco2 cell monolayers. The diet containing 3-aminobenzoic acid (3-ABA) was identified using liquid chromatography with quadrupole time-of-flight mass spectrometry. The abundance of fecal 3-ABA was compared between UC patients and healthy individuals followed by 16S rRNA metagenomic analysis to estimate the gut microbial function in ABA degradation. The anti-inflammatory effect of 3-ABA was examined in a mouse model of dextran sodium sulfate-induced colitis. ResultsStimulation with 3-ABA reduced epithelial permeability and enhanced barrier integrity in Caco2 cells by modulating the tight junctional regulatory pathway. 3-ABA was abundant in beans and decreased in the feces of UC patients. Functional prediction analysis of gut microbiota revealed an accelerated degradation of ABA with significant up-regulation of mabA, a gene encoding a bacterial enzyme involved in 3-ABA degradation, in UC patients. Rectal and oral administration of 3-ABA ameliorated experimental colitis in mice. Conclusion3-ABA abundant in beans enhanced intestinal epithelial integrity and ameliorated experimental colitis in mice. Proactive intake of 3-ABA might be a novel treatment approach for UC.

molecular biology↗

bioRxiv2024

Microtubules ensure transport of vegetative nuclei and sperm cells by fine-tuning their home positions

The pollen tube plays a pivotal role in double fertilization by delivering sperm cells (SCs) to the ovule. In Arabidopsis thaliana, a pair of SCs tightly connects with the vegetative nucleus (VN) to form the male germ unit (MGU), which is located in the apical region during pollen-tube growth, keeping the VN ahead of the SCs. MGU transport relies on independent motility of VN and SC pairs. However, the complexity of this dual motive force has hindered our understanding of MGU behavior, including its positioning and nuclear order. We used Arabidopsis mutants or transgenic plants that produced semi-motile MGUs with aberrant VNs or SCs to analyze the positioning of VN or SCs after stochastically disconnecting the MGU. In pollen tubes with an immotile SC pair, the VN was [~]70 m away from the tip, whereas in pollen tubes with an immotile VN, the SC pair was [~]100 m away from the tip, implying that the VN and SCs have independent home positions. The position of MGU moved forward owing to the loss of the microtubule-destabilizing kinesin KINESIN-13A. Conversely, microtubule depolymerization by oryzalin treatment or introducing mutations in TUBULIN BETA 4 (TUB4) deregulated the position of the MGU and shifted its position backward. In addition, tub4 plants exhibited reduced fertility. These data indicate a significant role of microtubules in stable MGU positioning to ensure reproductive success.

plant biology↗

bioRxiv2024

Diverse GABA signaling in the inner retina enables spatiotemporal coding

Summary paragraphGABA ({psi}-aminobutyric acid) is the primary inhibitory neurotransmitter in the mammalian central nervous system (CNS) 1,2. There is a wide range of GABAergic neuronal types, each of which plays an important role in neural processing and the etiology of neurological disorders 3-5. However, there is no comprehensive understanding of this functional diversity, due to the lack of genetic tools to target and study the multitude of cell types. Here we perform two-photon imaging of GABA release in the inner plexiform layer (IPL) of the mouse retina using the newly developed GABA sensor iGABASnFR2. By applying varied light stimuli to isolated retinae, we reveal over 40 different GABA-releasing neurons, including some not previously described. Individual types show unique distributions of synaptic release sites in the sublayers comprising the IPL, allowing layer-specific visual encoding. Synaptic input and output sites are aligned along specific retinal orientations for multiple neuronal types. Furthermore, computational modeling reveals that the combination of cell type-specific spatial structure and unique release kinetics enables inhibitory neurons to suppress and sculpt excitatory signals in response to a wide range of behaviorally relevant motion structures. Our high-throughput approach provides the first comprehensive physiological characterization of inhibitory signaling in the vertebrate CNS. Future applications of this method will enable interrogation of the function and dysfunction of diverse inhibitory circuits in health and disease.

neuroscience↗

bioRxiv2023

Establishment of the Meyer-Overton correlation in an artificial membrane without protein

BackgroundThe potency of anesthetics with various structures increases exponentially with lipophilicity, which is the Meyer-Overton (MO) correlation discovered over 120 years ago. The MO correlation was also observed with various biological effects and various chemicals, including alcohols; thus, the correlation represents a fundamental relationship between chemicals and organisms. The MO correlation was explained by the lipid and protein theories, although the debate has not been resolved and the principle remains unknown. MethodsThe gentle hydration method was used to form giant unilamellar vesicles (GUVs) consisting of high- and low-melting phospholipids and cholesterol in the presence of n-alcohols (C2-C12). Confocal fluorescence microscopy was used to determine the percentage of GUVs with domains in relation to the concentrations of n-alcohols. Resultsn-Alcohols inhibited the domain formation of GUVs, and the half inhibitory concentration (IC50) in the aqueous phase decreased exponentially with increasing chain length (lipophilicity). In contrast, the membrane concentrations of alcohols for the inhibition, which is a product of the membrane-water partition coefficient and the IC50 values, remained constant irrespective of the chain length. ConclusionsThe MO correlation is established in artificial lipid membrane, which supports the lipid theory. When alcohols reach the same critical concentration in the membrane, similar biological effects appear irrespective of the chain length, which is the principle underlying the MO correlation. Summary Statementn-Alcohols inhibit the domain formation of giant unilamellar vesicles according to the Meyer-Overton correlation.

biophysics↗

bioRxiv2023

A chromosome-level genome assembly of amodel conifer plant, the Japanese cedar,Cryptomeria japonica D. Don

Japanese cedar (Cryptomeria japonica D. Don) is the most important Japanese forest tree, occupying about 44% of artificial forests in Japan, and planted in East Asia, Azores Archipelago, and some islands in the Indian Ocean. Although the huge genome of the species (ca. 11 Gb) with abundant repeat elements might have been an obstacle for genetic analysis, the species is easily propagated by cutting, flowered by plant hormones like gibberellic acid, transformed by agrobacterium, and edited by CRISPR/Cas9. These characteristics of C. japonica are preferable to make the species a model conifer for which reference genome sequences are necessary. In this study, we report the first chromosome-level assembly for C. japonica (2n = 22) using a third generation selfed progeny with an estimated homozygosity of 0.96. Young leaf tissue was used to extract high-molecular-weight DNA (>50 kb) for HiFi PacBio long read sequencing and to construct Hi-C/Omni-C library for Illumina short read sequencing. Using the 29x and 26x genome coverage of HiFi and Illumina reads, respectively, de novo assembly resulted in 2,650 contigs (9.1 Gb in total) with N50 contig size of 12.0 Mb. The Hi-C analysis mapped 97% of the nucleotides on the 11 chromosomes. The assembly was verified by comparing with a consensus linkage map of 7,785 markers. The BUSCO analysis confirmed ~91% of conserved genes. Annotations of genes, repeat elements and synteny with other Cupressaceae and Pinaceae species were performed, providing fundamental resources for genomic research of conifers.

genomics↗