Biology subjects

Yeh, H.

Publications and source records attributed to Yeh, H..

11 recordsLinked to original sources

bioRxiv2025

Sex specific correction of maternal inflammation-induced behavioral abnormalities by the inhibition of colony-stimulating factor 1 receptor

We have previously reported the therapeutic effect of depletion and regeneration of endogenous microglia on autism spectrum disorder-like behaviors in offspring from the dams under maternal immune activation (MIA) by dampening their neuritogenic activation. Here we show a long-lasting pathological effect by MIA, leading to abnormal behaviors in offspring mice in a sex-specific manner at 3 months of age. MIA was induced by injecting Polyinosinic:polycytidylic acid [Poly(I:C)] at 10mg/kg at E9.5 with preselected dams based on the immunoreactivity to low-dose Poly(I:C) injection. MIA offspring show impairments in sociability, repetitive behavior, and spatial working and associative memories in both sexes, whereas only male offspring show social novelty deficit. MIA has no effect on anxiety-like behavior nor sensori-motor or locomotor activity. Administering colony stimulating factor receptor (CSF1R) inhibitor in young adult MIA offspring regenerates microglia and ameliorates sociability deficits in males and spatial working and associative memory impairments in both sexes without effect on social novelty impairments. Transcriptomic analysis of prefrontal cortex and hippocampal tissues reveals MIA and sex-specific pathways and highlights potential key genes involved in the corrective effect of microglial regeneration in MIA offspring. Our results underscore the potential of the sex-specific therapeutic applications of CSF1R inhibitor for MIA-related social and cognitive disorders.

animal behavior and cognition↗

bioRxiv2025

Atypical antipsychotics alter microglial functions via astrocyte-derived extracellular vesicles

A limited understanding of the underlying molecular mechanisms of atypical antipsychotics has hindered efforts to develop the next generation of treatments for schizophrenia. In particular, there has been little investigation of how medications like clozapine and olanzapine modulate human non-neuronal cells, including astrocytes and microglia. Recent postmortem and serum-based studies suggest that schizophrenia etiology involves dysregulated cellular communication through extracellular vesicles (EVs). Astrocytes are a major source of these EVs and are strongly implicated in the etiology of schizophrenia by convergent data from human postmortem, brain imaging, RNA-sequencing, and genome-wide association studies. We hypothesized that clozapine and olanzapine can affect microglia biology indirectly via astrocytic secretion of EVs. We used in vitro cellular models with primary human astrocytes and PBMC-derived microglial-like cells to investigate the downstream impact of isolated astrocyte-derived EVs (ADEVs) on microglial phenotypes relevant to schizophrenia, including microglial phagocytosis, motility, and morphology. To model microglia-mediated synaptic pruning in vitro, we utilized image-based quantification of microglia engulfment of isolated human synaptosomes. We found that treatment with ADEVs reduced microglial synaptosome phagocytosis in a dose-dependent manner. This reduction was reversed upon addition of ADEVs isolated from astrocytes treated with norclozapine or olanzapine. ADEVs isolated from clozapine-treated astrocytes increased microglial motility, indicating that clozapine alters microglial surveillance activity without affecting phagocytosis through these ADEVs. Together, these results suggest that atypical antipsychotics have distinct and indirect impact on microglia biology mediated by ADEVs. These results highlight a potentially critical role for ADEVs in regulating glial cell communication and suggest they may be promising therapeutic targets for next-generation antipsychotic development.

neuroscience↗

bioRxiv2024

Identifying brain-penetrant small molecule modulators of human microglia using a cellular model of synaptic pruning

Microglia dysregulation is implicated across a range of neurodevelopmental and neurodegenerative disorders, making their modulation a promising therapeutic target. Using PBMC-derived induced microglia-like cells (piMGLCs) in a scalable assay, we screened 489 CNS-penetrant compounds for modulation of microglial phagocytosis of human synaptosomes in a validated assay for microglia-mediated synaptic pruning. Compounds from the library that reduced phagocytosis by [≥]2 standard deviations across the library without cytotoxicity were validated in secondary screens, with 28 of them further confirmed to reduce phagocytosis by 50% or more. Image-based morphological measurements were calculated to measure the degree of ramified vs. amoeboid morphotype as an indicator of activation state. Additionally, transcriptomic profiling indicated divergent effects on cell signaling, metabolism, activation, and actin dynamics across confirmed compounds. In particular, multiple CNS-penetrant small molecules with prior FDA approval or demonstration of safety in vivo demonstrated modulatory effects on microglia. These potential disease-modifying agents represent high-priority candidates for repositioning studies in neurodevelopmental, neuroinflammatory, or neurodegenerative disorders.

neuroscience↗

bioRxiv2024

Natural Language Prompts Guide the Design of Novel Functional Protein Sequences

The advent of natural language interaction with machines has ushered in new innovations in text-guided generation of images, audio, video, and more. In this arena, we introduce Biological Multi-Modal Model (BioM3), as a novel framework for designing functional proteins via natural language prompts. This framework integrates natural language with protein design through a three-stage process: aligning protein and text representations in a joint embedding space learned using contrastive learning, refinement of the text embeddings, and conditional generation of protein sequences via a discrete autoregressive diffusion model. BioM3 synthe-sizes protein sequences with detailed descriptions of the protein structure, lineage, and function from text annotations to enable the conditional generation of novel sequences with desired attributes through natural language prompts. We present in silico validation of the model predictions for subcellular localization prediction, reaction classification, remote homology detection, scaffold in-painting, and structural plausibility, and in vivo and in vitro experimental tests of natural language prompt-designed synthetic analogs of Src-homology 3 (SH3) domain proteins that mediate signaling in the Sho1 osmotic stress response pathway in bakers yeast. BioM3 possesses state-of-the-art performance in zero-shot prediction and homology detection tasks, and generates proteins with native-like tertiary folds and wild-type levels of experimentally assayed function.

synthetic biology↗

bioRxiv2024

Illumination mediates a switch in both active sensing and control in weakly electric fish

To execute sensory-guided behavior, the nervous system must manage uncertainty within multiple streams of information. There are two highly nonlinear mechanisms for achieving this: 1) sensory reweighting, an internal neural computation which places more emphasis on sensory information that exhibits the least uncertainty, e.g. in a Bayesian framework, and 2) active sensing, an overt behavior that seeks to improve the quality of sensory information before it enters the nervous system. Here we show that animals solve both of these nonlinear problems concurrently. We studied how the weakly electric glass knifefish Eigenmannia virescens alters its movement dynamics under parametric manipulations of illumination. We hypothesized a concomitant switch in both overt active sensing and internal multisensory reweighting. To test this, we varied illumination levels from 0.1 to 210 lx as fish tracked a moving refuge. We discovered that in a neighborhood of a critical threshold (on the order of 1 to 10 lx), small increases in illumination led to dramatic changes in both active sensing and multisensory control, specifically in 1) steep reductions in fish head and tail movements and 2) decreased refuge tracking phase lag. Outside of this threshold, large changes in illumination only caused small changes in active sensing and control. A control-theoretic model that dynamically modulates the weights of vision and electrosense due to illumination changes corroborates our findings. These findings underscore the complex, multipartite, nonlinear nature of locomotor control and the remarkable ability of the nervous system to execute multiple parallel strategies for managing sensory uncertainty.

animal behavior and cognition↗

bioRxiv2024

Optimization of liver graft function using a poly-pharmacological drug cocktail CEPT in a simulated transplant model

BackgroundThe number of patients in need of a liver transplant far exceeds the supply of available organs. This imbalance could be dramatically reduced should the donor organ pool be expanded by rendering marginal cases transplantable rather than discarded. The poly-pharmacological drug cocktail CEPT (Chroman-1, Emricasan, Polyamine, and Trans-ISRIB (integrated stress inhibitor)) has been found to improve the in-vitro viability of human pluripotent stem cells (hPSCs) following cryopreservation. It is worth exploring CEPTs ability to inhibit various apoptotic pathways and preserve cellular function for potentially mitigating warm ischemic stress of the anhepatic phase of graft implantation and promoting more rapid graft recovery following reperfusion with continuous treatment. MethodsRat livers without warm ischemia and CEPT supplementation are the healthy control: fresh (n=3) group. Room-temperature warm ischemia was used to replicate the anhepatic phase of graft implantation in the control (n=6) group and the experimental CEPT group (n=6) without and with CEPT supplementation, respectively. Transplantation was modeled by ex-vivo reperfusion at 37{degrees}C for six hours with Williams E-based hepatocyte culture media and with CEPT supplementation in the CEPT group. ResultsLivers treated with CEPT during warm ischemia and subsequent reperfusion have improved hepatocellular function as indicated by increased oxygen O2 utilization, stable pH, and improved cholangiocyte function indicated by the increased hourly rate of bile production. Furthermore, resistance, an endothelial injury marker, and caspase 3/7, an apoptotic marker, were lower. ConclusionTo improve the utilization of available donor livers, different stages of the organ transplantation process can be optimized. The anhepatic phase, which includes the period from the removal of the native liver from the recipient to the reperfusion of the donors graft liver through the portal vein during graft implantation, can be targeted using CEPT for mitigating warm ischemia-induced injury that occurs during vascular anastomosis. (S1 Fig: Graphical abstract)

bioengineering↗

bioRxiv2024

Impaired glycolysis in aged endothelial cells is associated with reduced neovascularisation upon tissue ischemia

The vascular system experiences an age-associated decline in tissue perfusion and response to ischemic diseases. The factors driving this age-associated neovascularization decline remain unclear. While old endothelial cells (ECs) adopt a pro-angiogenic gene expression profile, we observed a stark reduction in the proliferative capacity of old ECs, while migratory capabilities remain intact. This is paralleled by a drastic decline in glycolytic capacity and ATP production, which likely act as limiting factors to neovascularization. These findings may provide new strategies to restore EC function in aging, thereby improving organ resilience and extending health- and lifespan.

molecular biology↗

bioRxiv2022

Loss of function in the autism and schizophrenia-associated gene CYFIP1 in human microglia supports a role in synaptic pruning

BackgroundThe CYFIP1 gene, located in the neurodevelopmental risk locus 15q11.2, is highly expressed in microglia, but its role in human microglial function as it relates to neurodevelopment is not well understood. MethodsWe generated multiple CRISPR knockouts of CYFIP1 in patient-derived models of microglia to characterize function and phenotype. Using microglia-like cells reprogrammed from peripheral blood mononuclear cells, we quantified phagocytosis of synaptosomes (isolated and purified synaptic vesicles) from human iPSC-derived neuronal cultures as an in vitro model of synaptic pruning. We repeated these analyses in human iPSC-derived microglia, and characterized microglial development and function through morphology and motility. ResultsCYFIP1 knockout using orthogonal CRISPR constructs in multiple patient-derived cell lines was associated with statistically significant decrease in synaptic vesicle phagocytosis in microglia models derived from both PBMCs and iPSCs (p<0.0001). Morphology was also shifted toward a more ramified profile (p<0.0001), and motility was significantly reduced (p<0.0001). However, iPSC-CYFIP1 knockout lines retained the ability to differentiate to functional microglia. Conclusion: The changes in microglial phenotype and function from loss of CYFIP1 may contribute to pruning abnormalities observed in CYFIP1-associated neurodevelopmental disorders. Investigating risk genes in a range of CNS cell types may be required to fully understand the way in which common and rare variants intersect to yield neuropsychiatric disorders.

neuroscience↗

bioRxiv2022

Masked inverse folding with sequence transfer for protein representation learning

AO_SCPLOWBSTRACTC_SCPLOWSelf-supervised pretraining on protein sequences has led to state-of-the art performance on protein function and fitness prediction. However, sequence-only methods ignore the rich information contained in experimental and predicted protein structures. Meanwhile, inverse folding methods reconstruct a proteins amino-acid sequence given its structure, but do not take advantage of sequences that do not have known structures. In this study, we train a masked inverse folding protein masked language model parameterized as a structured graph neural network. During pretraining, this model learns to reconstruct corrupted sequences conditioned on the backbone structure. We then show that using the outputs from a pretrained sequence-only protein masked language model as input to the inverse folding model further improves pretraining perplexity. We evaluate both of these models on downstream protein engineering tasks and analyze the effect of using information from experimental or predicted structures on performance.

bioengineering↗

bioRxiv2021

The role of antifreeze glycopeptides (AFGP) and polyvinyl alcohol/polyglycerol (X/Z-1000) cocktails as ice modulators during partial freezing of rat livers.

The current liver organ shortage has pushed the field of liver transplantation to develop new methods to prolong the preservation time of livers from the current clinical standard of static cold storage. Our approach, termed partial freezing, aims to induce a thermodynamically stable frozen state at deeper storage temperatures (-10{degrees}C to -15{degrees}C) than can be achieved with supercooling, while simultaneously maintaining a sufficient unfrozen fraction to limit dehydration and ice damage. This research first demonstrated that partially frozen glycerol treated rat livers were functionally similar after thawing from either -10 or -15{degrees}C with respect to subnormothermic machine perfusion metrics and histology. Next, we assessed the effect of adding either of two ice modulators, antifreeze glycoprotein (AFGP) and a polyvinyl alcohol/polyglycerol combination (X/Z-1000), on the viability and structural integrity of partially frozen rat livers compared to glycerol-only control livers. Results showed that AFGP livers had high levels of ATP and the least edema but suffered from significant endothelial cell damage. X/Z-1000 livers had the highest levels of ATP and energy charge (EC) but also demonstrated endothelial damage and post-thaw edema. Glycerol-only control livers exhibited the least DNA damage on Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining but also had the lowest levels of ATP and EC. Further research is necessary to optimize the ideal ice modulator cocktail for our partial-freezing protocol. Modifications to cryoprotective agent (CPA) combinations, as well as improvements to machine perfusion CPA loading and unloading, can help improve the viability of these partially frozen organs.

physiology↗

bioRxiv2019

The NKCC1 antagonist bumetanide mitigates interneuronopathy associated with ethanol exposure In utero

Prenatal exposure to ethanol induces aberrant tangential migration of corticopetal GABAergic interneurons, and long-term alterations in the form and function of the prefrontal cortex. We have hypothesized that interneuronopathy contributes significantly to the pathoetiology of fetal alcohol spectrum disorders (FASD). Activity-dependent tangential migration of GABAergic cortical neurons is driven by depolarizing responses to ambient GABA present in the cortical enclave. We found that ethanol exposure potentiates the depolarizing action of GABA in GABAergic cortical interneurons of the embryonic mouse brain. Pharmacological antagonism of the cotransporter NKCC1 mitigated ethanol-induced potentiation of GABA depolarization and prevented aberrant patterns of tangential migration induced by ethanol in vitro. In a model of FASD, maternal bumetanide treatment prevented interneuronopathy in the prefrontal cortex of ethanol exposed offspring, including deficits in behavioral flexibility. These findings position interneuronopathy as a mechanism of FASD symptomatology, and posit NKCC1 as a pharmacological target for the management of FASD.

developmental biology↗