Biology subjects

Liao, C.

Publications and source records attributed to Liao, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Psilocybin Prolongs the Neurovascular Coupling Response in Mouse Visual Cortex

Psilocybin has profound therapeutic potential for various mental health disorders, but its mechanisms of action are unknown. Functional MRI studies have reported the effects of psilocybin on brain activity and connectivity; however, these measurements rely on neurovascular coupling to infer neural activity changes and assume that blood flow responses to neural activity are not altered by psilocybin. Using two-photon excited fluorescence imaging in the visual cortex of awake mice to simultaneously measure neural activity and capillary blood flow dynamics, we found that psilocybin administration prolonged the increase in visual stimulus-evoked capillary blood flow - an effect which was reduced by pretreatment with a 5-HT2AR antagonist - despite not causing changes in the stimulus-evoked neural response. Multi-modal widefield imaging also showed that psilocybin extends the stimulus-evoked vascular responses in surface vessels with no observed effect on the population neural response. Computational simulation with a whole-brain neural mass model showed that prolonged neurovascular coupling responses can lead to spurious increases in BOLD-based measures of functional connectivity. Together, these findings demonstrate that psilocybin broadens neurovascular responses in the brain and highlights the importance of accounting for these effects when interpreting human neuroimaging data of psychedelic drug action.

neuroscience↗

bioRxiv2025

MuSHIN: A multi-way SMILES-based hypergraph inference network for metabolic model reconstruction

Genome-scale metabolic models (GEMs) are indispensable tools for probing cellular metabolism, enabling predictions of metabolic fluxes, guiding strain optimization, and advancing biomedical research. However, their predictive capacity is often compromised by incomplete reaction networks, stemming from gaps in biochemical knowledge, annotation inaccuracies, and insufficient experimental validations. Here we present MuSHIN (Multi-way SMILES-based Hypergraph Interface Network), a novel deep hypergraph learning method that integrates network topology with biochemical domain knowledge to predict missing reactions in GEMs. Evaluated on 926 high- and intermediate-quality GEMs with artificially removed reactions, MuSHIN significantly outperforms state-of-the-art methods, achieving up to a 17% improvement across multiple metrics and maintaining robust recovery even under severe network sparsity. Furthermore, MuSHIN substantially enhances phenotypic predictions in 24 draft GEMs associated with fermentation by resolving critical metabolic gaps, as validated against experimental measurements. Together, these findings highlight MuSHINs potential to advance GEM reconstruction and accelerate discoveries in systems biology, metabolic engineering, and precision medicine.

bioinformatics↗

bioRxiv2025

Effects of diffusion MRI spatial resolution on human brain short-range association fiber reconstruction and structural connectivity estimation

Short-range association fibers (SAFs) are critical for cortical communications but are often underestimated in conventional resolution diffusion magnetic resonance imaging (dMRI) since they locate within a [~]1.5mm thin layer of superficial white matter. With the emergence of high-resolution diffusion imaging techniques, this study timely evaluated the effects of image spatial resolution on SAF reconstruction using simulation data and multi-resolution (2, 1.5, and 0.96 mm iso.) empirical data acquired on the same 20 healthy subjects using the gSlider sequence and 20 widely used tractography approaches. Resolution effects were qualitatively assessed through model fitting and tractography results and quantitatively evaluated using global and regional short-range connectivity strength (SCS). It is found that lower resolution systematically reduces SCS across all methods in a spatially varying manner. Moreover, tractography methods exhibit significant differences in resolution sensitivity, with diffusion tensor imaging (DTI) based single-tissue single-fiber tractography showing greater vulnerability than constrained spherical deconvolution (CSD)-based multi-tissue multi-fiber tractography. Probabilistic tracking with anatomical constraints (ACT) and filtering (SIFT) improves robustness. Finally, up-sampling data to nominally higher resolution partially mitigates resolution-induced degradation and improves SAF reconstruction accuracy, particularly for DTI tractography. Based on these findings, higher resolution and multi-shell imaging is recommended if possible. For a given dataset, data up-sampling and DTI-based probabilistic tracking with ACT is recommended for single-shell low b-value data. CSD-based probabilistic tracking with ACT and SIFT is recommended for single-shell higher b-value data and multi-shell data. In summary, this study systematically and quantitatively evaluated resolution effects on SAF reconstruction and structural connectivity estimation and provided practical guidelines for more accurate mapping of SAFs. These advances hold promises to improve the characterization of healthy and diseased human brains in a wide range of neuroscientific and clinical applications.

neuroscience↗

bioRxiv2025

Functional loss of CHS2 confers high levels resistance to Bacillus thuringiensis Vip3Aa, but with significant fitness costs in five lepidopteran species

Bacillus thuringiensis (Bt) crops, engineered to produce insecticidal proteins such as Vip3Aa and Cry toxins, have revolutionized pest management by providing a sustainable alternative to chemical pesticides. However, the development of resistance to these toxins has driven the investigation of underlying mechanisms to better understand how pests evade toxicity and to develop more effective resistance management strategies. Recently, a laboratory-selected Spodoptera frugiperda strain exhibited a high level of resistance to Vip3Aa (resistance ratio: 5562-fold), with the mutation of the chitin synthase gene, SfCHS2, identified as a key factor. In this study, we extend these findings to additional lepidopteran species, including Spodoptera exigua and Agrotis ipsilon. Our results show that CHS2 knockout strains lack the peritrophic matrix (PM), while the resistant Sfru_R3 strain retains its PM. Knockout of this gene resulted in high levels resistance to Vip3Aa. These findings further validate the role of the CHS2 gene in Vip3Aa resistance and highlight its potential as a target for resistance management in lepidopteran pests. This study advances our understanding of the molecular mechanisms behind resistance to Vip3Aa and supports the development of strategies to delay resistance in Bt crop management.

genetics↗

bioRxiv2025

Lithium partially rescues gene expression and enhancer activity from heterozygous knockout of AKAP11 while inducing novel differential changes

Bipolar disorder (BD) is a complex psychiatric condition usually requiring long-term treatment. Lithium (Li) remains the most effective mood stabilizer for BD, yet it benefits only a subset of patients, and its precise mechanism of action remains elusive. Exome sequencing has identified AKAP11 (A-kinase anchoring protein 11) as a shared risk gene for BD and schizophrenia (SCZ). Given that both the AKAP11-Protein Kinase A (PKA) complex and Li target and inhibit Glycogen Synthase Kinase-3 beta (GSK3{beta}), we hypothesize that Li may partially normalize the transcriptomic and/or epigenomic alterations observed in heterozygous AKAP11-knockout (Het-AKAP11-KO) iPSC-derived neurons. In this study, we employed genome-wide approaches to assess the effects of Li on the transcriptome and epigenome of human iPSC-derived Het-AKAP11-KO neuronal culture. We show that chronic Li treatment in this cellular model upregulates key pathways that were initially downregulated by Het-AKAP11-KO, several of which have also been reported as downregulated in synapses of BD and SCZ post-mortem brain tissues. Moreover, we demonstrated that Li treatment partially rescues certain transcriptomic alterations resulting from Het-AKAP11-KO, bringing them closer to the WT state. We suggest two possible mechanisms underlying these transcriptomic effects: (1) Li modulates histone H3K27ac levels at intergenic and intronic enhancers, influencing enhancer activity and transcription factor binding, and (2) Li enhances GSK3{beta} serine 9 phosphorylation, impacting WNT/{beta}-catenin signaling and downstream transcription. These findings underscore Lis potential as a therapeutic agent for BD and SCZ patients carrying AKAP11 loss-of-function variants or exhibiting similar pathway alterations to those observed in Het-AKAP11-KO models.

genomics↗

bioRxiv2025

A robust platform streamlining aromatic noncanonical amino acid biosynthesis and genetic code expansion in E. coli

Genetic code expansion has significantly enhanced the diversity and functionality of proteins in the biological world, leading to a wide range of applications in catalysis, biology, and medicine. Despite the extraordinary advances in genetic code expansion over the past years, the availability and cost of noncanonical amino acids (ncAAs) remain one of the major obstacles, particularly for large-scale industrial production. In situ biosynthesis of ncAAs from commercially available precursors offers a promising solution to this challenge, yet only a few biosynthetic pathways for specific amino acids have been reported to date. To address this gap, we present a robust platform that couples the biosynthesis of aromatic amino acids with genetic code expansion in E. coli, enabling the production of proteins and peptides containing incorporated ncAAs. Forty amino acids with diverse functional groups were synthesized from aryl aldehydes by a biosynthetic pathway comprising two heterologously expressed enzymes and one endogenous enzyme. Nineteen of these amino acids were successfully incorporated into superfolder GFP (sfGFP) using three classic orthogonal translation systems. The platforms versatility was further demonstrated by the production of macrocyclic peptides and antibodies containing functional ncAAs, such as para-azidophenylalanine and para-boronophenylalanine. We envision that the simplicity, efficiency, compatibility, and broad applicability of this biosynthetic pathway and the platform will greatly facilitate the production of peptides, enzymes, and antibodies containing ncAAs, thereby accelerating their use in various applications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/631627v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@8a6d2eorg.highwire.dtl.DTLVardef@5f8b9org.highwire.dtl.DTLVardef@c514aorg.highwire.dtl.DTLVardef@acd66d_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Single-nucleus transcriptomics reveals time-dependent and cell-type-specific effects of psilocybin on gene expression

There is growing interest to investigate classic psychedelics and ketamine as therapeutics for mental illnesses. Previous studies have demonstrated that one dose of psilocybin or ketamine leads to persisting neural and behavioral changes. The durability of these effects suggests that there are likely alterations in gene expression at the transcriptional level. In this study, we performed single-nucleus RNA sequencing of the dorsal medial frontal cortex of male and female mice. Samples were collected at 1, 2, 4, 24, or 72 hours after psilocybin or ketamine administration and from control animals. At baseline, major subtypes of excitatory and GABAergic neurons selectively express particular serotonin receptor transcripts. The psilocybin-evoked differentially expressed genes in excitatory neurons are involved in synaptic plasticity, distinct from genes enriched in GABAergic neurons, which contribute to mitochondrial function and cellular metabolism, and non-neuronal glial cells. The effect of psilocybin on gene expression is time-dependent, including an early phase at 1 hour followed by a late phase at 72 hours of transcriptional response after administration, and differs from the changes following ketamine administration, which peaks at 2 - 4 hours. Collectively, the results provide a resource for understanding the cell type-specific and time-dependent changes in gene expression induced by psilocybin and ketamine in the mouse medial frontal cortex, which may underpin the drugs long-term effects on neural circuits and behavior.

neuroscience↗

bioRxiv2024

Pyramidal cell types and 5-HT2A receptors are essential for psilocybin's lasting drug action

Psilocybin is a serotonergic psychedelic with therapeutic potential for treating mental illnesses1-4. At the cellular level, psychedelics induce structural neural plasticity5,6, exemplified by the drug-evoked growth and remodeling of dendritic spines in cortical pyramidal cells7-9. A key question is how these cellular modifications map onto cell type-specific circuits to produce psychedelics behavioral actions10. Here, we use in vivo optical imaging, chemogenetic perturbation, and cell type-specific electrophysiology to investigate the impact of psilocybin on the two main types of pyramidal cells in the mouse medial frontal cortex. We find that a single dose of psilocybin increased the density of dendritic spines in both the subcortical-projecting, pyramidal tract (PT) and intratelencephalic (IT) cell types. Behaviorally, silencing the PT neurons eliminates psilocybins ability to ameliorate stress-related phenotypes, whereas silencing IT neurons has no detectable effect. In PT neurons only, psilocybin boosts synaptic calcium transients and elevates firing rates acutely after administration. Targeted knockout of 5-HT2A receptors abolishes psilocybins effects on stress-related behavior and structural plasticity. Collectively these results identify a pyramidal cell type and the 5-HT2A receptor in the medial frontal cortex as playing essential roles for psilocybins long-term drug action.

neuroscience↗

bioRxiv2024

Telocytes link epithelial nutrient sensing with amplification of the ILC2-tuft cell circuit

Group 2 innate lymphocytes (ILC2s) are prevalent in small intestine but engagement of type 2 immunity during basal processes are incompletely described. Thymic stromal lymphopoietin (TSLP), a cytokine implicated in ILC2 activation, was constitutively expressed in villus telocytes and crypt-associated trophocytes, specialized fibroblasts that sustain epithelial identity. Feeding increased TSLP and induced ILC2 type 2 cytokines that were attenuated by deletion of TSLP in PDGFR+ stromal cells or TSLP receptor on ILC2s. Mouse and human telocytes expressed receptors for glucagon-like peptide-2 (GLP-2), which is released by enteroendocrine cells (EECs) after eating. GLP-2 induced intestinal TSLP, TSLP-dependent ILC2 cytokine production, and tuft cell hyperplasia. The telocyte-alarmin relay couples EEC nutrient detection with amplification of a tuft cell chemosensory circuit that diversifies surveillance of ingested cargo. One-Sentence SummaryIntestinal telocyte TSLP relays signals from enteroendocrine cells to ILC2s to amplify the tuft cell circuit in response to feeding.

immunology↗

bioRxiv2024

A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner

We deployed the Blended Genome Exome (BGE), a DNA library blending approach that generates low pass whole genome (1-4x mean depth) and deep whole exome (30-40x mean depth) data in a single sequencing run. This technology is cost-effective, empowers most genomic discoveries possible with deep whole genome sequencing, and provides an unbiased method to capture the diversity of common SNP variation across the globe. To evaluate this new technology at scale, we applied BGE to sequence >53,000 samples from the Populations Underrepresented in Mental Illness Associations Studies (PUMAS) Project, which included participants across African, African American, and Latin American populations. We evaluated the accuracy of BGE imputed genotypes against raw genotype calls from the Illumina Global Screening Array. All PUMAS cohorts had R2 concordance [≥]95% among SNPs with MAF[≥]1%, and never fell below [≥]90% R2 for SNPs with MAF<1%. Furthermore, concordance rates among local ancestries within two recently admixed cohorts were consistent among SNPs with MAF[≥]1%, with only minor deviations in SNPs with MAF<1%. We also benchmarked the discovery capacity of BGE to access protein-coding copy number variants (CNVs) against deep whole genome data, finding that deletions and duplications spanning at least 3 exons had a positive predicted value of [~]90%. Our results demonstrate BGE scalability and efficacy in capturing SNPs, indels, and CNVs in the human genome at 28% of the cost of deep whole-genome sequencing. BGE is poised to enhance access to genomic testing and empower genomic discoveries, particularly in underrepresented populations.

genomics↗

bioRxiv2024

Thermophilic Fungus Uses Anthraquinones to Modulate Ferrous Excretion, Sterol-Mediated Endocytosis and Iron Storage in Response to Cold Stress

To date, there is no real physiological mechanisms for iron excretion in eukaryote, and no physiological "actuator" that can control all the three fundamental biologic processes of absorption, storage and excretion. Here we observed that the accumulation of anthraquinones by Thermomyces dupontii under cold stress can achieve this process. Through mutation analysis, we found that mutant {Delta}An deficiency in anthraquinones accumulated ferrous and total free iron due to adopting a rare lifestyle with no endocytosis but accumulation of membrane-derived vesicles. Anthraquinone complement indicated that the vesicles in {Delta}An could coat the extrinsic anthraquinone-induced granules to prevent contact with the fungal interiors. Detailed chemical investigation on {Delta}An led to characterization of a rare oxygen-free ergosterene with unstable nature in air as the major membrane steroid in {Delta}An, suggesting hypoxia inner in {Delta}An cells, consistent with dramatically low oxygen-consuming rates in {Delta}An. A series of physiological and metabolic analysis indicated anthraquinones were involved in exporting ferrous and promoting formation of oxygen-containing metabolites, including ergosterols for endocytosis and iron chelators for iron storage. Moreover, we found that both the anticancer agent mitoxantrone with well know-cardiotoxicity side effect and the major terpenoid-derived polycyclic aromatics from Danshen for treating cardiovascular disease showed potent ferrous transporting capabilities in human cancer cells. Our findings provide a novel insight into the underlying mechanisms of polycyclic aromatics in nature and pharmacology, and offer new strategy for developing potential therapeutics and agents for membrane transport, iron homestasis and anticold. Graphical AbstractUp to now, regulation of iron homeostasis by metabolites have rarely been characterized. Moreover, no excretory mechanisms for iron in fungi have been reported. In this study, we found that Thermomyces dupontii can accumulate a large amount of anthraquinones under cold stress. The anthraquinones can release free ferric ion, reduce ferric to ferrous ions, and export ferrous ions, greatly enhancing thermophilic fungus to survive in the bio-system environment. Furthermore, lack of the anthraquinones can inhibit oxygen-dependent ergosterol mediated endocytosis, leading to an self-imposed isolation via oxygen-free ergosterene-mediated cell membranes. Importantly, the well known anthraquinone compound Mitoxantraquinone for anticancer and the main terpenoid polycyclic aromatic metabolites in traditional Chinese medicine Danshen for the treatment of cardiovascular diseases both exhibit strong ferrous ions transport capabilities. Our findings provided new insights for developing potential therapies and drugs for iron homeostasis and drug delivery. O_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC="FIGDIR/small/605589v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@114551eorg.highwire.dtl.DTLVardef@1e03589org.highwire.dtl.DTLVardef@dad51borg.highwire.dtl.DTLVardef@dd0601_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Fast and reliable quantitative measures of white matter development with magnetic resonance fingerprinting

Developmental cognitive neuroscience aims to shed light on evolving relationships between brain structure and cognitive development. To this end, quantitative methods that reliably measure individual differences in brain tissue properties are fundamental. Standard qualitative MRI sequences are influenced by scan parameters and hardware-related biases, and also lack physical units, making the analysis of individual differences problematic. In contrast, quantitative MRI can measure physical properties of the tissue but with the cost of long scan durations and sensitivity to motion. This poses a critical limitation for studying young children. Here, we examine the reliability and validity of an efficient quantitative multiparameter mapping method - Magnetic Resonance Fingerprinting (MRF) - in children scanned longitudinally. We focus on T1 values in white matter, since quantitative T1 values are known to primarily reflect myelin content, a key factor in brain development. Forty-nine children aged 8-13y (mean 10.3y {+/-}1.4) completed two scanning sessions 2-4 months apart. In each session, two 2-minute 3D-MRF scans at 1mm isotropic resolution were collected to evaluate the effect of scan duration on image quality and scan-rescan reliability. A separate calibration scan was used to measure B0 inhomogeneity and correct for bias. We examined the impact of scan time and B0 inhomogeneity correction on scan-rescan reliability of values in white matter, by comparing single 2-min and combined two 2-min scans, with and without B0-correction. Whole-brain voxel-based reliability analysis showed that combining two 2-min MRF scans improved reliability (pearsons r=0.87) compared with a single 2-min scan (r=0.84), while B0-correction had no effect on reliability in white matter (r=0.86 and 0.83 4-min vs 2-min). Using diffusion tractography, we delineated MRF-derived T1 profiles along major white matter fiber tracts and found similar or higher reliability for T1 from MRF compared to diffusion parameters (based on a 10-minute dMRI scan). Lastly, we found that T1 values in multiple white matter tracts were significantly correlated with age. In sum, MRF-derived T1 values were highly reliable in a longitudinal sample of children and replicated known age effects. Reliability in white matter was improved by longer scan duration but was not affected by B0-correction, making it a quick and straightforward scan to collect. We propose that MRF provides a promising avenue for acquiring quantitative brain metrics in children and patient populations where scan time and motion are of particular concern.

neuroscience↗

bioRxiv2024

Classification of psychedelic drugs based on brain-wide imaging of cellular c-Fos expression

Psilocybin, ketamine, and MDMA are psychoactive compounds that exert behavioral effects with distinguishable but also overlapping features. The growing interest in using these compounds as therapeutics necessitates preclinical assays that can accurately screen psychedelics and related analogs. We posit that a promising approach may be to measure drug action on markers of neural plasticity in native brain tissues. We therefore developed a pipeline for drug classification using light sheet fluorescence microscopy of immediate early gene expression at cellular resolution followed by machine learning. We tested male and female mice with a panel of drugs, including psilocybin, ketamine, 5-MeO-DMT, 6-fluoro-DET, MDMA, acute fluoxetine, chronic fluoxetine, and vehicle. In one-versus-rest classification, the exact drug was identified with 67% accuracy, significantly above the chance level of 12.5%. In one-versus-one classifications, psilocybin was discriminated from 5-MeO-DMT, ketamine, MDMA, or acute fluoxetine with >95% accuracy. We used Shapley additive explanation to pinpoint the brain regions driving the machine learning predictions. Our results support a novel approach for characterizing and validating psychoactive drugs with psychedelic properties.

neuroscience↗

bioRxiv2024

The landscape of gene loss and missense variation across the mammalian tree informs on gene essentiality

BackgroundThe degree of gene and sequence preservation across species provides valuable insights into the relative necessity of genes from the perspective of natural selection. Here, we developed novel interspecies metrics across 462 mammalian species, GISMO (Gene identity score of mammalian orthologs) and GISMO-mis (GISMO-missense), to quantify gene loss traversing millions of years of evolution. GISMO is a measure of gene loss across mammals weighed by evolutionary distance relative to humans, whereas GISMO-mis quantifies the ratio of missense to synonymous variants across mammalian species for a given gene. RationaleDespite large sample sizes, current human constraint metrics are still not well calibrated for short genes. Traversing over 100 million years of evolution across hundreds of mammals can identify the most essential genes and improve gene-disease association. Beyond human genetics, these metrics provide measures of gene constraint to further enable mammalian genetics research. ResultsOur analyses showed that both metrics are strongly correlated with measures of human gene constraint for loss-of-function, missense, and copy number dosage derived from upwards of a million human samples, which highlight the power of interspecies constraint. Importantly, neither GISMO nor GISMO-mis are strongly correlated with coding sequence length. Therefore both metrics can identify novel constrained genes that were too small for existing human constraint metrics to capture. We also found that GISMO scores capture rare variant association signals across a range of phenotypes associated with decreased fecundity, such as schizophrenia, autism, and neurodevelopmental disorders. Moreover, common variant heritability of disease traits are highly enriched in the most constrained deciles of both metrics, further underscoring the biological relevance of these metrics in identifying functionally important genes. We further showed that both scores have the lowest duplication and deletion rate in the most constrained deciles for copy number variants in the UK Biobank, suggesting that it may be an important metric for dosage sensitivity. We additionally demonstrate that GISMO can improve prioritization of recessive disorder genes and captures homozygous selection. ConclusionsOverall, we demonstrate that the most constrained genes for gene loss and missense variation capture the largest fraction of heritability, GISMO can help prioritize recessive disorder genes, and identify the most conserved genes across the mammalian tree. O_FIG O_LINKSMALLFIG WIDTH=168 HEIGHT=200 SRC="FIGDIR/small/594531v1_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@11c3e46org.highwire.dtl.DTLVardef@13c6e70org.highwire.dtl.DTLVardef@76a6c7org.highwire.dtl.DTLVardef@1bf8d86_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2024

A type II secreted subtilase from commensal rhizobacteria disarms the immune elicitor peptide flg22

Plant roots grow in association with a community of microorganisms collectively known as the rhizosphere microbiome. Immune activation in response to elicitors like the flagellin-derived epitope flg22 restricts bacteria on plant roots but also inhibits plant growth. Some commensal root-associated bacteria are capable of suppressing the plant immune response to elicitors. In this study, we investigated the ability of 165 root-associated bacteria to suppress flg22-induced immune activation and growth restriction. We demonstrate that a type II secreted subtilase, which we term Immunosuppressive Subtilase A (IssA), from Dyella japonica strain MF79 cleaves the immune eliciting peptide flg22 and contributes to immune suppression. IssA homologs are found in other plant-associated commensals, with particularly high conservation in the order Xanthomonadales. This represents a novel mechanism by which commensal microbes modulate flg22-induced immunity in the rhizosphere microbiome.

microbiology↗

bioRxiv2024

The landscape of regional missense mutational intolerance quantified from 125,748 exomes

Missense variants can have a range of functional impacts depending on factors such as the specific amino acid substitution and location within the gene. To interpret their deleteriousness, studies have sought to identify regions within genes that are specifically intolerant of missense variation. Here, we leverage the patterns of rare missense variation in 730,947 exome sequenced individuals in the Genome Aggregation Database (gnomAD v4.1.1) against a null mutational model to identify transcripts with regional differences in missense constraint. Missense-depleted regions are enriched for ClinVar pathogenic variants, de novo missense variants from individuals with neurodevelopmental disorders, and complex trait heritability. Following ClinGen calibration recommendations for the ACMG/AMP variant classification guidelines, we establish that variants within regions with <36% of their expected missense variation achieve moderate support for pathogenicity. We integrate this regional constraint measure into a missense deleteriousness metric (named MPC) that effectively stratifies rare and de novo missense variants in individuals with early-onset developmental conditions from controls. These results provide additional tools to aid in missense variant interpretation.

genomics↗

bioRxiv2024

Uncovering microstructural architecture from histology

Mapping the brains fiber network is crucial for understanding its function and malfunction, but resolving nerve trajectories over large fields of view is challenging. Here, we show that computational scattered light imaging (ComSLI) can map fiber networks in histology independent of sample preparation, also in formalin-fixed paraffin-embedded (FFPE) tissues including whole human brain sections. We showcase this method in new and archived, animal and human brain sections, for different sample preparations (in paraffin, deparaffinized, various stains, unstained fresh-frozen). We convert microscopic orientations to microstructure-informed fiber orientation distributions (FODs). Adapting tractography tools from diffusion magnetic resonance imaging (dMRI), we trace axonal trajectories revealing white and gray matter connectivity. These allow us to identify altered microstructure or deficient tracts in demyelinating or neurodegenerating pathology, and to show key advantages over dMRI, polarization microscopy, and structure tensor analysis. Finally, we map fibers in non-brain tissues, including muscle, bone, and blood vessels, unveiling the tissues function. Our cost-effective, versatile approach enables micron-resolution studies of intricate fiber networks across tissues, species, diseases, and sample preparations, offering new dimensions to neuroscientific and biomedical research.

pathology↗

bioRxiv2024

Neuroprotective Effects of Bioactive Molecules Derived from Tobacco as Potential Therapeutic Candidates for Alzheimer Disease

Neurodegenerative diseases are significant global health challenges, particularly with an aging population. While tobacco is traditionally linked to health risks, recent studies suggest it may contain compounds beneficial for neurodegenerative conditions. Herein, we explore the potential of bioactive compounds in tobacco as neuroprotective agents for Alzheimers disease (AD). Using genetic engineering, we developed a novel approach with neural progenitor cells (NPCs) derived from embryonic stem cells, equipped with an NF-{kappa}B reporter system to screen tobacco extracts. Our screenings identified three compounds with significant inhibitory effects on NF-{kappa}B activation, a key mediator of neuroinflammation in AD. Among these, rutin exhibited profound neuroprotective effects in an NPC damage model induced by Amyloid-{beta}25-35, reducing apoptotic cell death, enhancing cellular proliferation, and activating critical survival signaling pathways. This modulation underlies rutins anti-inflammatory and neuroprotective activities. Together, our findings support the potential of tobacco-derived compounds in AD therapy and lay the foundation for further exploration of their pharmaceutical value.

pharmacology and toxicology↗