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Biology subjects

Shinoda, K.

Publications and source records attributed to Shinoda, K..

13 recordsLinked to original sources

A novel subset of hepatocytes is simultaneously gluconeogenic and de novo lipogenic in the fed state and is naturally insulin resistant

It is generally accepted that hepatic gluconeogenesis, the synthesis of glucose from non-carbohydrate substrates is active in the fasted state and inactive in the fed state. In contrast, de novo lipogenesis is active in the fed state and is inactive in the fasted state. Here, we used targeted single cell RNA-seq, HCR RNA-FISH, and PrimeFlow in normal physiological mouse liver, and identified a subpopulation of periportal hepatocytes that simultaneously co-express both gluconeogenic and lipogenic genes in the fed state. Euglycemic-hyperinsulinemic clamps further demonstrated that this novel hepatocyte subpopulation is naturally insulin resistant. Spatial metabolic imaging coupled with stable isotope tracing analyses revealed individual hepatocytes that simultaneously undergo both gluconeogenesis and de novo lipogenesis. These dual-positive hepatocytes were also present in human hepatocytes from humanized mouse livers. Moreover, the number of dual-positive hepatocytes increased in high-fat diet-fed mice, suggesting a paradigm shift in our understanding of how the liver becomes insulin resistant.

molecular biology↗

Transcriptional Heterogeneity Reveals a Synaptic Gene Program in Developing and Adult Human Oligodendrocyte Precursor Cells

Human oligodendrocyte precursor cells (OPCs) arise early in gestation and expand broadly during cortical development, yet the extent of their heterogeneity remains poorly defined. Here, we isolated >2,300 highly pure OPCs from post-conceptional week (PCW) 17 human cortex using an optimized PDGFR-based immunopanning and performed single-cell RNA sequencing. Unsupervised clustering revealed four transcriptionally distinct embryonic OPC subsets, including a previously unrecognized population that expressed genes linked to synaptic development, synaptic signaling, and neuromodulation. This subset - designated embryonic synaptic OPCs (eSyn-OPCs) - comprised approximately 28.5% of all embryonic OPCs in the cortex and was characterized by robust expression of synapse-associated secreted factors (THBS2, WNT5A, WNT7A, PLAT, ACHE) and multiple neurotransmitter receptor subunits. Histological analyses across PCW 12-22 demonstrated that eSyn-OPCs first appear around PCW 15 and are enriched in proliferative germinal zones. Spatial transcriptomics confirmed their localization near neural stem and progenitor cells, suggesting proximal neuron-OPC communication during early cortical assembly. Purified eSyn-OPCs differentiated into mature oligodendrocytes in vitro, confirming their oligodendrocyte lineage identity. Reanalysis of adult human single-nucleus RNA-seq datasets uncovered a transcriptionally analogous OPC subset (adult synaptic OPCs, aSyn-OPCs), though with reduced representation of structural synaptic genes and neurotransmitter receptor diversity compared to eSyn-OPCs. Together, these results identify a synaptically specialized OPC population in both developing and adult human cortex and reveal that eSyn-OPCs possess unexpectedly rich synaptic signaling machinery. These findings suggest that human OPCs may participate directly in neuron-glia communication during early cortical development and raise the possibility of developmental stage-specific roles for eSyn-OPCs in shaping neural circuit formation.

neuroscience↗

Longitudinal multimodal characterization of radiation dermatitis in the C57BL/6J mouse model

Radiation dermatitis (RD) is a frequent and therapy-limiting toxicity of cancer radiotherapy, yet its mechanistic basis remains poorly understood. To address the need for quantitative, mechanistic insight, we developed a longitudinal C57BL/6J mouse model integrating clinical grading, non-invasive biophysical ("mesoscopic") measurements, histopathology, and bulk transcriptomics. This controlled design enabled pseudo-longitudinal analysis of inflammation, barrier dysfunction, and fibrosis across four weeks after a single 25 Gy exposure. Transcriptomic profiling revealed early activation of phagosome formation, MHC I antigen presentation, and neutrophil degranulation preceding visible skin injury, followed by enrichment of IL-1, IL-10, and IL-13 signaling at peak disease. Mesoscopic erythema, fibrosis, and transepidermal water loss each displayed distinct temporal and molecular signatures, with limited overlap among gene sets. Histologic scoring confirmed early epidermal and inflammatory responses, linked to extracellular matrix remodeling and vascular development. The observed pathways align with prior studies implicating IL-17 and a senescence-associated IL-6/CCR6 axis, extending these findings into a quantitative, time-resolved framework. This multimodal resource bridges molecular, morphological, and functional scales, providing a platform for mechanistic and therapeutic studies of RD.

genomics↗

Astringent flavanol fires the locus-noradrenergic system, regulating neurobehavior and autonomic nerves

Astringent flavanols (FLs) have shown enhanced cognitive function in a large intervention trial, but their mechanism remains unclear due to poor bioavailability. An oral dose of FLs increased spontaneous locomotion and memory, with activation of the sympathetic-adrenergic-medullary (SAM) and hypothalamic-pituitary-adrenal (HPA) axis, as shown by increased urinary catecholamine concentrations and corticotropin-releasing hormone (CRH) mRNA expression in the paraventricular nucleus (PVN) of mice. MS imaging showed high intensity of noradrenaline (NA) in the locus coeruleus (LC), which plays a key role in learning and memory, the hypothalamus lateral preoptic area, which affects sleep and arousal, and the brainstem as the origin of the sympathetic nervous system, immediately after FLs administration. Subsequent in situ hybridization (ISH) analysis showed that these NAs originated from LC. Astringent compounds like FLs influence brain function and physiological changes. Furthermore, the present series of results presents novel mechanisms by which food sensory properties maintain homeostasis. Highlights- A oral dose of astringent flavanols (FLs) immediately fires locus coeruleus-noradrenaline axis - FLs enhance spontaneous locomotion and short-term memory in mice - SAM and HPA axis are also activated by an oral dose of FLs - FLs astringency affects the brain and body, contributing to homeostasis.

synthetic biology↗

Widespread discordance between mRNA expression, protein abundance and de novo lipogenesis activity in hepatocytes during the fed-starvation transition

The mammalian liver plays a critical role in maintaining metabolic homeostasis during fasting and feeding. Liver function is further shaped by sex dimorphism and zonation of hepatocytes. To explore how these factors interact, we performed deep RNA-sequencing and label-free proteomics on periportal and pericentral hepatocytes isolated from male and female mice under fed and starved conditions. We developed a classification system to assess protein-mRNA relationship and found that gene products (mRNA or protein) for most zonation markers showed strong concordance between mRNA and protein. Although classical growth hormone regulated sex-biased gene products also exhibited concordance, [~]60% of sex-biased gene products showed protein-level enrichment without corresponding mRNA differences. In contrast, transition between feeding and starvation triggered widespread changes in mRNA expression without significantly affecting protein levels. In particular, key lipogenic mRNAs (e.g. Acly, Acaca, and Fasn) were dramatically induced by feeding, but their corresponding proteins (ACLY, ACC1, and FAS) showed little to no change even as functional de novo lipogenic activity increased [~]28-fold in the fed state. To facilitate further exploration of these findings, we developed Discorda (https://shinoda-lab.shinyapps.io/discorda/), a web database for interactive analysis. Our findings reinforce the principle that mRNA changes do not reliably predict corresponding protein levels (and vice versa), particularly in the context of sex and acute metabolic regulation of hepatocytes, and that de novo lipogenesis activity can be completely uncoupled from changes in protein expression.

bioinformatics↗

Speech Synthesis from Electrocorticogram During Imagined Speech Using a Transformer-Based Decoder and Pretrained Vocoder

Synthesizing speech from Electrocorticogram (ECoG) signals recorded during imagined speech remains a challenge due to the absence of synchronized audio signals for training. To address this, we propose a training framework that utilizes audio recorded during overt speech tasks as a surrogate ground truth for imagined speech signals, based on the consistency of the linguistic content. We employed a Transformer-based decoder to generate log-mel spectrograms from imagined speech ECoG, which were then converted into waveform audio using a pre-trained Parallel WaveGAN. In experiments involving ECoG recordings from 13 participants, the synthesized speech achieved dynamic time warping-aligned Pearson correlation coefficients ranging from 0.74 to 0.84 with the proxy targets. These results demonstrate that overt speech audio can serve as an effective training target for reconstructing imagined speech, offering a viable solution for training decoders in the absence of behavioral output.

neuroscience↗

In vivo-Active Soluble Epoxide Hydrolase-targeting PROTACs with Improved Potency and Stability

Soluble epoxide hydrolase (sEH) is a bifunctional enzyme involved in fatty acid metabolism and promising drug target. We previously reported first-generation sEH proteolysis-targeting chimeras (PROTACs) with limited degradation potency and low aqueous and metabolic stability. Herein, we report the development of next-generation sEH PROTAC molecules with improved stability and degradation potency. One of the most potent molecules (compound 8) exhibits a half-maximal degradation concentration in the sub-nM range, is stable in vivo, and effectively degrades sEH in mouse livers and brown adipose tissues. Given the role played by sEH in many metabolic and nonmetabolic diseases, the presented molecules provide useful chemical probes for the study of sEH biology. They also hold potential for therapeutic development against a range of disease conditions, including diabetes, inflammation, and metabolic disorders.

biochemistry↗

Spatial hepatocyte plasticity of gluconeogenesis during the metabolic transitions between fed, fasted and starvation states

The liver acts as a master regulator of metabolic homeostasis in part by performing gluconeogenesis. This process is dysregulated in type 2 diabetes, leading to elevated hepatic glucose output. The parenchymal cells of the liver (hepatocytes) are heterogeneous, existing on an axis between the portal triad and the central vein, and perform distinct functions depending on location in the lobule. Here, using single cell analysis of hepatocytes across the liver lobule, we demonstrate that gluconeogenic gene expression (Pck1 and G6pc) is relatively low in the fed state and gradually increases first in the periportal hepatocytes during the initial fasting period. As the time of fasting progresses, pericentral hepatocyte gluconeogenic gene expression increases, and following entry into the starvation state, the pericentral hepatocytes show similar gluconeogenic gene expression to the periportal hepatocytes. Similarly, pyruvate-dependent gluconeogenic activity is approximately 10-fold higher in the periportal hepatocytes during the initial fasting state but only 1.5-fold higher in the starvation state. In parallel, starvation suppresses canonical beta-catenin signaling and modulates expression of pericentral and periportal glutamine synthetase and glutaminase, resulting in an enhanced pericentral glutamine-dependent gluconeogenesis. These findings demonstrate that hepatocyte gluconeogenic gene expression and gluconeogenic activity are highly spatially and temporally plastic across the liver lobule, underscoring the critical importance of using well-defined feeding and fasting conditions to define the basis of hepatic insulin resistance and glucose production.

molecular biology↗

Feasibility of decoding covert speech in ECoG with aTransformer trained on overt speech

Several attempts for speech brain-computer interfacing (BCI) have been made to decode phonemes, sub-words, words, or sentences using invasive measurements, such as the electrocorticogram (ECoG), during auditory speech perception, overt speech, or imagined (covert) speech. Decoding sentences from covert speech is a challenging task. Sixteen epilepsy patients with intracranially implanted electrodes participated in this study, and ECoGs were recorded during overt speech and covert speech of eight Japanese sentences, each consisting of three tokens. In particular, Transformer neural network model was applied to decode text sentences from covert speech, which was trained using ECoGs obtained during overt speech. We first examined the proposed Transformer model using the same task for training and testing, and then evaluated the models performance when trained with overt task for decoding covert speech. The Transformer model trained on covert speech achieved an average token error rate (TER) of 46.6% for decoding covert speech, whereas the model trained on overt speech achieved a TER of 46.3% (p > 0.05; d = 0.07). Therefore, the challenge of collecting training data for covert speech can be addressed using overt speech. The performance of covert speech can improve by employing several overt speeches.

neuroscience↗

Neuronal Enhancers are Hotspots For DNA Single-Strand Break Repair

Genome stability is essential for all cell types. However, defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons. The neuronal genome is subjected to a constant barrage of endogenous DNA damage due to high levels of oxidative metabolism in the central nervous system. Surprisingly, we know little about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here, we show that neurons, but not other post-mitotic cells, accumulate unexpectedly high numbers of DNA single-strand breaks (SSBs) at specific sites within the genome. These recurrent SSBs are found within enhancers, and trigger DNA repair through recruitment and activation of poly(ADP-ribose) polymerase-1 (PARP1) and XRCC1, the central SSB repair scaffold protein. Notably, deficiencies in PARP1, XRCC1, or DNA polymerase {beta} elevate the localized incorporation of nucleotides, suggesting that the ongoing DNA synthesis at neuronal enhancers involves both short-patch and long-patch SSB repair processes. These data reveal unexpected levels of localized and continuous DNA single-strand breakage in neurons, suggesting an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.

neuroscience↗

The Dystonia Gene THAP1 Controls DNA Double Strand Break Repair Choice

The Shieldin complex, consisting of SHLD1, SHLD2, SHLD3 and REV7, shields DNA double strand breaks (DSBs) from nucleolytic resection. The end-protecting activity of Shieldin promotes productive non-homologous end joining (NHEJ) in G1 but can threaten genome integrity during S-phase by blocking homologous recombination (HR). Curiously, the penultimate Shieldin component, SHLD1 is one of the least abundant mammalian proteins. Here, we report that the transcription factors THAP1, YY1 and HCF1 bind directly to the SHLD1 promoter, where they cooperatively maintain the low basal expression of SHLD1. Functionally, this transcriptional network ensures that SHLD1 protein levels are kept in check to enable a proper balance between end protection and end resection during physiological DSB repair. In the context of BRCA1 deficiency, loss of THAP1 dependent SHLD1 expression confers cross resistance to PARP inhibitor and cisplatin, and shorter progression free survival in ovarian cancer patients. In contrast, loss of THAP1 in BRCA2 deficient cells increases genome instability and correlates with improved responses to chemotherapy. Pathogenic THAP1 mutations are causatively linked to the adult-onset torsion dystonia type 6 (DYT6) movement disorder, but the critical disease targets are unknown. We further demonstrate that murine models of Thap1-associated dystonia show reduced Shld1 expression concomitant with elevated levels of unresolved DNA damage in the brain. In summary, our study provides the first example of a transcriptional network that directly controls DSB repair choice and reveals a previously unsuspected link between DNA damage and dystonia.

molecular biology↗

A new lipid force field (FUJI)

To explore inhomogeneous and anisotropic systems such as lipid bilayers, the Lennard-Jones particle mesh Ewald (LJ-PME) method was applied without a traditional isotropic dispersion correction. As the popular AMBER and CHARMM lipid force fields were developed using a cutoff scheme, their lipid bilayers unacceptably shrank when using LJ-PME method. A new lipid force field (FUJI) was developed on the basis of the AMBER force field scheme including the Lipid14 van der Waals parameters. Point charges were calculated by the restrained electrostatic potentials of many lipid conformers. The torsion energy profiles were calculated by high level ab initio molecular orbitals (LCCSD(T)/Aug-cc-pVTZ//LMP2/Aug-cc-pVTZ); then, the molecular mechanical dihedral parameters were derived by means of a fast Fourier transform. Incorporating these parameters into a new lipid force field without any fittings to experimental data, desirable lipid characteristics such as the area per lipid and lateral diffusion coefficients were obtained by GROMACS molecular dynamics simulations using the LJ-PME method and hydrogen virtual sites. The stability and structures of large membranes with undulatory fluctuations were studied by a multidrug efflux transporter (AcrABZ-TolC) with inner and outer membranes.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/373183_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (92K):\norg.highwire.dtl.DTLVardef@12cf574org.highwire.dtl.DTLVardef@a6cdbforg.highwire.dtl.DTLVardef@10dbd16org.highwire.dtl.DTLVardef@f8fd3a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

Tumor cell-adipocyte gap junctions activate lipolysis and are essential for breast tumorigenesis

A pro-tumorigenic role for adipocytes has been identified in breast cancer, and reliance on fatty acid catabolism found in aggressive tumors. The molecular mechanisms by which tumor cells coopt neighboring adipocytes, however, remain elusive. Here, we describe a direct interaction linking tumorigenesis to adjacent adipocytes. We examine breast tumors and their normal adjacent tissue from several patient cohorts, patient-derived xenografts and mouse models, and find that lipolysis and lipolytic signaling are activated in neighboring adipose tissue. We find that functional gap junctions form between breast cancer cells and adipocytes. As a result, cAMP is transferred from breast cancer cells to adipocytes and activates lipolysis in a gap junction-dependent manner. We identify connexin 31 (GJB3), which promotes receptor triple negative breast cancer growth and activation of lipolysis in vivo. Thus, direct tumor cell-adipocyte interaction contributes to tumorigenesis and may serve as a new therapeutic target in breast cancer. One sentence summaryGap junctions between breast cancer cells and adipocytes transfer cAMP and activate lipolysis in the breast tumor microenvironment to support growth.

cancer biology↗