Search bioRxiv⌕ Search

Biology subjects

He, Y.

Publications and source records attributed to He, Y..

At least 343 records · Page 19Linked to original sources

ARHGAP32 as a novel RhoGAP interacting with desmoplakin is required for desmosomal organization and assembly

Desmosomes are specialized cell-cell junctions that play a critical role in maintaining tissue barrier integrity, particularly in mechanically stressed tissues. The assembly of desmosomes is regulated by the cytoskeleton and its regulators, and desmosomes also function as a central hub for regulating F-actin. However, the specific mechanisms underlying the crosstalk between desmosomes and F-actin, particularly involving RhoGAP or RhoGEF proteins, remain unclear. In our study, we identified that ARHGAP32, a Rho GTPase-activating protein, is located in desmosomes through its interaction with DSP via its GAB2-interacting domain. Using CRISPR-Cas9 gene knockout system, we confirmed that ARHGAP32 is required for proper desmosomal organization, maturation, and length regulation. Notably, the loss of ARHGAP32 resulted in increased formation of F-actin stress fibers and phosphorylation of MYOSIN at T18/S19, indicating enhanced actomyosin contractility. Furthermore, inhibition of ROCK1 kinase activity using Y27632 effectively restored desmosomal organization. Moreover, we demonstrated that the regulation of desmosomes by ARHGAP32 is crucial for maintaining the integrity of epithelial cell sheets. Collectively, our study unveils ARHGAP32 as a RhoGAP present at desmosomes, potentially facilitating the crosstalk between desmosomes and F-actin. Its presence is indispensable for desmosomal assembly and the preservation of epithelial cell sheet integrity by regulating actomyosin contractility.

cell biology↗

Dendritic cell-derived lncRNA in patients with acute coronary syndrome

BackgroundLong non-coding RNA (lncRNA) and dendritic cells (DC) play an important role in the occurrence and development of acute coronary syndrome (ACS). However, the role and mechanism of DC-derived lncRNA in patients with ACS still remains understudied. ObjectiveTo investigate the expression difference and role of lncRNA in monocyte-derived DC(moDC) in patients with acute coronary syndrome(ACS). Methods and ResultsThe subjects were divided into 4 groups: (1) healthy control group (CON), (2) unstable angina group (UA), (3) non-ST elevation myocardial infarction group (NSEMI or NST) and (4) ST elevation myocardial infarction group (STEMI or ST). Peripheral blood was extracted and isolated to obtain mononuclear cells (PBMC). After induction into moDC, morphology was observed by electron microscope and identified by flow cytometry (FCM) (CD80, CD86, CD11c, CD14, HLA-DR), and morphological and functional differences were compared. The differentially expressed lncRNA were screened by gene sequencing, and the biological functions of which were predicted by GO and KEGG and the correlation between candidate lncRNA and target genes was analyzed. The expression levels of markers, signaling pathways, inflammatory factors and target gene were performed by FCM, RT-PCR, WB and ELISA after the candidate lncRNA were over-expressed or silenced. Electron microscope showed that the cells were suspended cells of dendritic pseudopodia. FCM showed that the expression levels of DC markers CD11c (99.02{+/-}0.12%) and HLA-DR (99.32{+/-}0.08%) were high, while the expression levels of CD80 (24.27{+/-}0.99%) and CD86 (32.38{+/-}0.59%) were low. The number of differentially expressed lncRNA screened by gene sequencing was as follows: CON vs UA, 3; CON vs. NST, 49; CON vs ST, 35; UA vs. NST, 115; UA vs ST, 113; ST vs NST, 4. The results of FCM, RT-PCR, WB and ELISA showed that the expression levels of markers (CD80, CD86, HLA-DR), signaling pathways (p-PI3K, p-AKT), inflammatory factors (IL-6 and IL-12p70) and target gene (CCL14) were increased after over-expression of CCL15-CCL14; On the contrary, its expression level was decreased. ConclusionsThere are differences in moDC morphology and function and lncRNA expression in different types of ACS patients, and the differentially expressed lncRNA (CCL15-CCL14) regulates the function of moDC.

immunology↗

Torques within and outside the human spindle balance twist at anaphase

At each cell division, nanometer-scale motors and microtubules give rise to the micron-scale spindle. Many mitotic motors step helically around microtubules in vitro, and most are predicted to twist the spindle in a left-handed direction. However, the human spindle exhibits only slight global twist, raising the question of how these molecular torques are balanced. Here, using lattice light sheet microscopy, we find that anaphase spindles in the epithelial cell line MCF10A have a high baseline twist, and we identify factors that both increase and decrease this twist. The midzone motors KIF4A and MKLP1 are redundantly required for left-handed twist at anaphase, and we show that KIF4A generates left-handed torque in vitro. The actin cytoskeleton also contributes to left-handed twist, but dynein and its cortical recruitment factor LGN counteract it. Together, our work demonstrates that force generators regulate twist in opposite directions from both within and outside the spindle, preventing strong spindle twist during chromosome segregation.

cell biology↗

Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning

The ability to measure gene expression at single-cell resolution has elevated our understanding of how biological features emerge from complex and interdependent networks at molecular, cellular, and tissue scales. As technologies have evolved that complement scRNAseq measurements with things like single-cell proteomic, epigenomic, and genomic information, it becomes increasingly apparent how much biology exists as a product of multimodal regulation. Biological processes such as transcription, translation, and post-translational or epigenetic modification impose both energetic and specific molecular demands on a cell and are therefore implicitly constrained by the metabolic state of the cell. While metabolomics is crucial for defining a holistic model of any biological process, the chemical heterogeneity of the metabolome makes it particularly difficult to measure, and technologies capable of doing this at single-cell resolution are far behind other multiomics modalities. To address these challenges, we present GEFMAP (Gene Expression-based Flux Mapping and Metabolic Pathway Prediction), a method based on geometric deep learning for predicting flux through reactions in a global metabolic network using transcriptomics data, which we ultimately apply to scRNAseq. GEFMAP leverages the natural graph structure of metabolic networks to learn both a biological objective for each cell and estimate a mass-balanced relative flux rate for each reaction in each cell using novel deep learning models.

bioinformatics↗

Aberration correction for deformable mirror based remote focusing enables high-accuracy whole-cell super-resolution imaging

Single-molecule localization microscopy (SMLM) enables three-dimensional (3D) investigation of nanoscale structures in biological samples, offering unique insights into their organization. However, traditional 3D super-resolution microscopy using high numerical aperture (NA) objectives is limited by imaging depth of field (DOF), restricting their practical application to relatively thin biological samples. Here, we developed a unified solution for thick sample super-resolution imaging using a deformable mirror (DM) which was served for fast remote focusing, optimized point spread function (PSF) engineering and accurate aberration correction. By effectively correcting the system aberrations introduced during remote focusing and sample aberrations at different imaging depths, we achieved high-accuracy, large DOF imaging of the whole-cell organelles [i.e. nuclear pore complex (NPC), microtubules, and mitochondria] with a nearly uniform resolution of approximately 30 nm across the entire cellular volume.

bioengineering↗

Vaxign-DL: A Deep Learning-based Method for Vaccine Design and its Evaluation

Reverse vaccinology (RV) provides a systematic approach to identifying potential vaccine candidates based on protein sequences. The integration of machine learning (ML) into this process has greatly enhanced our ability to predict viable vaccine candidates from these sequences. We have previously developed a Vaxign-ML program based on the eXtreme Gradient Boosting (XGBoost). In this study, we further extend our work to develop a Vaxign-DL program based on deep learning techniques. Deep neural networks assemble non-linear models and learn multilevel abstraction of data using hierarchically structured layers, offering a data-driven approach in computational design models. Vaxign-DL uses a three-layer fully connected neural network model. Using the same bacterial vaccine candidate training data as used in Vaxign-ML development, Vaxign-DL was able to achieve an Area Under the Receiver Operating Characteristic of 0.94, specificity of 0.99, sensitivity of 0.74, and accuracy of 0.96. Using the Leave-One-Pathogen-Out Validation (LOPOV) method, Vaxign-DL was able to predict vaccine candidates for 10 pathogens. Our benchmark study shows that Vaxign-DL achieved comparable results with Vaxign-ML in most cases, and our method outperforms Vaxi-DL in the accurate prediction of bacterial protective antigens.

bioinformatics↗

A multistage, dual voxel study of glutamate in the anterior cingulate cortex in schizophrenia supports a primary pyramidal dysfunction model of disorganization

BackgroundSchizophrenia is an illness where glutamatergic dysfunction in the anterior cingulate cortex (ACC) has been long suspected; Recent in vivo evidence (Adams et al. 2022) has implicated pyramidal dysfunction (reduced glutamate tone) as the primary pathophysiology contributing to subtle features, with a secondary disinhibition effect (higher glutamate tone) resulting in the later emergence of prominent clinical symptoms. We investigate if genetic high risk (GHR) for schizophrenia reduces glutamatergic tone in ACC when compared to the states of clinical high risk (CHR) and first episode schizophrenia (FES) where symptoms are already prominent. MethodsWe recruited 302 individuals across multiple stages of psychosis (CHR, n=63; GHR, n=76; FES, n=96) and healthy controls (n=67) and obtained proton magnetic resonance spectroscopy of glutamate from perigenual ACC (pACC) and dorsal ACC (dACC) using 3-Tesla scanner. ResultsGHR had lower Glu compared to CHR while CHR had higher Glu compared to FES and HC. Higher disorganization burden, but not any other symptom domain, was predicted by lower levels of Glu in the GHR group (dACC and pACC) and in the CHR group (pACC only). ConclusionsThe reduction in glutamatergic tone in GHR supports the case for a pyramidal dysfunction contributing to higher disorganization, indicating disorganization to be the core domain in the pathophysiology of schizophrenia. Higher glutamate (likely due to disinhibition) is apparent when psychotic symptoms are raising to be prominent (CHR), though at the full-blown stage of psychosis, the relationship between glutamate and symptoms ceases to be a simple linear one.

neuroscience↗

A genome-wide association study of neonatal metabolites

The hereditary component significantly influences the concentration of metabolites in adults. Nevertheless, the precise influence of genetic factors on neonatal metabolites remains uncertain. To bridge this gap, we employed genotype imputation techniques on large-scale low-pass genome data obtained from non-invasive prenatal testing. Subsequently, we conducted association studies on a total of 75 metabolic components in neonates. The study identified a total 17 previous reported associations and 13 novel discovered associations between single nucleotide polymorphisms and metabolic components. These associations were initially found in the discovery cohort (8,744 participants) and subsequently confirmed in a replication cohort (19,041 participants). The average heritability of metabolic components was calculated to be 76.2%, with a range of 69-78.8%. The aforementioned findings offer valuable insights pertaining to the genetic architecture of neonatal metabolism. In BriefLarge-scale genomes of maternal non-invasive prenatal testing provide insights into the genetic contribution to neonatal metabolism. HighlightsGWAS of 27,785 low-pass genomes revealed 13 novel associations of neonatal metabolic components. Estimated an average of 76.2% heritability of neonatal metabolic components and showed the individual concentration can be accurately predicted from polygenic risk scores. A total of 17 established relationships have been observed, providing evidence that maternal genomes can be utilized in neonatal metabolite GWAS.

genetics↗

Rapid and prolonged response of oligodendrocyte lineage cells in standard acute cuprizone demyelination model revealed by in situ hybridization

Dietary administration of a copper chelator, cuprizone (CPZ), has long been reported to induce intense and reproducible demyelination of several brain structures such as the corpus callosum (CC) in mice, followed by spontaneous remyelination after drug withdrawal. Despite the widespread use of CPZ as an animal model for demyelinating diseases such as multiple sclerosis (MS), the mechanism by which it induces demyelination and then allows robust remyelination is still unclear. An intensive mapping of the oligodendrocyte (OL) lineage cell dynamics during the de-and remyelination course would be of particular importance for a deeper understanding of this model. Here, using a panel of OL lineage cell markers as in situ hybridization (ISH) probes, including Pdgfra, Plp, Mbp, Mog, Enpp6, combined with immunofluorescence staining of CC1, SOX10, we provide a detailed dynamic profile of OL lineage cells during the entire course of the model from 3.5 days, 1, 2, 3, 4,5 weeks of CPZ treatment, i.e. the demyelination period, as well as after 1, 2, 3, 4 weeks of recovery (drug withdrawal) from 5 weeks of CPZ treatment, i.e. the remyelination period. The result showed an unexpected early death of mature OLs and response of OL progenitor cells (OPCs) in vivo upon CPZ challenge, and a prolonged upregulation of myelin-forming OLs compared to the intact control even 4 weeks after CPZ withdrawal. These data may point to the need to optimize the timing windows for the introduction of pro-remyelination therapies in demyelinating diseases such as MS, and may serve as a basic reference system for future studies of the effects of any intervention on demyelination and remyelination using the CPZ model.

neuroscience↗

Fast and accurate disulfide bridge detection

Recombinant expression of proteins, propelled by therapeutic antibodies, has evolved into a multi-billion-dollar industry. Essential here is quality control assessment of critical attributes such as sequence fidelity, proper folding, and post-translational modifications (PTMs). Errors can lead to diminished bioactivity and, in the context of therapeutic proteins, an elevated risk for immunogenicity. Over the years, many techniques were developed and applied to validate proteins in a standardized and high-throughput fashion. One parameter has, however, so far been challenging to assess. Disulfide bridges, covalent bonds linking two Cysteine residues, assist in the correct folding and stability of proteins and thus have a major influence on their efficacy. Mass spectrometry promises to be an optimal technique to uncover them in a fast and accurate fashion. In this work, we present a unique combination of sample preparation, data acquisition and analysis facilitating the rapid and accurate assessment of disulfide bridges in purified proteins. Through microwave-assisted acid hydrolysis (MAAH), the proteins are digested rapidly and artifact-free into peptides, with a substantial degree of overlap over the sequence. The nonspecific nature of this procedure, however, introduces chemical background which is efficiently removed by integrating ion mobility preceding the mass spectrometric measurement. The nonspecific nature of the digestion step additionally necessitates new developments in data analysis, for which we extended the XlinkX node in Proteome Discoverer (XlinkX/PD) to efficiently process the data and ensure correctness through effective false discovery rate correction. The entire workflow can be completed within one hour, allowing for high-throughput, high-accuracy disulfide mapping.

biochemistry↗

Structure of scavenger receptor SCARF1 and its interaction with lipoproteins

SCARF1 (Scavenger receptor class F member 1, SREC-1 or SR-F1) is a type I transmembrane protein that recognizes multiple endogenous and exogenous ligands such as modified low-density lipoproteins (LDL) and is important for maintaining homeostasis and immunity. But the structural information and the mechanisms of ligand recognition of SCARF1 are largely unavailable. Here we solve the crystal structures of the N-terminal fragments of human SCARF1, which show that SCARF1 forms homodimers and its epidermal growth factor (EGF)-like domains adopt a long-curved conformation. Then we examine the interactions of SCARF1 with lipoproteins and are able to identify a region on SCARF1 for recognizing modified LDLs. The mutagenesis data show that the positively charged residues in the region are crucial for the interaction of SCARF1 with modified LDLs, which is confirmed by making chimeric molecules of SCARF1 and SCARF2. In addition, teichoic acids, a cell wall polymer expressed on the surface of gram-positive bacteria, are able to inhibit the interactions of modified LDLs with SCARF1, suggesting the ligand binding sites of SCARF1 might be shared for some of its scavenging targets. Overall, these results provide mechanistic insights into SCARF1 and its interactions with the ligands, which are important for understanding its physiological roles in homeostasis and the related diseases.

biophysics↗

Dual long-axis reorganization of hippocampus in youth

The reorganization of human hippocampus, especially its interaction with cortex, remains largely undefined in youth. The organization of a single hippocampal long-axis has been predominantly characterized as monotonic1-6, despite recent indications of nonmonotonic features in neuron density7 and geometric eigenmodes8. While the human cortical hierarchy has been well recognized for significant developmental and evolutionary advantages9-12, hippocampus has been typically considered an evolutionarily conserved brain structure1,13,14, and overlooked regarding its integrative role of cortical hierarchical processing during development. Here, we corroborated the presence and significance of a dual long-axis representation of the hippocampal connectome and geometry including both linear and quadratic gradients along its long-axis in youth. This finding was robust across two independent large-scale developmental cohorts. Charting development of the dual long-axis gradients underscored their specific contributions to the cortical hierarchy maturation from the frontoparietal and salience/ventral attention networks. The observed developmental variability in spontaneous brain activities in youth parallels the gradients of myelin content. During childhood through adolescence to early adulthood, the hippocampus reorganized the dual long-axis by gradually relaxing its geometric constraints on the intrinsic network organization of cortical spontaneous activity for refined executive functions. Molecular processes underlying such reorganization of the dual long-axis in hippocampus are linked to neural growth, stress hormone regulation, and neuroactive signaling. Our findings enrich the understanding of hippocampal-cortical reorganizational principles across structural, functional, and molecular dimensions as well as its maturation, and define the plasticity distribution within the human hippocampus at systems level, holding potentials to enhance and translate neurodevelopment and neuropsychiatric healthcare.

neuroscience↗

Predicting gender from structural and functional connectomes via brain and population graph neural networks

Gender differences in terms of structural and functional organization of the human brain have been extensively studied, but existing works have mostly been limited to single modalities. In this paper, we propose a graph attention network architecture (BrainGAT) that uses informative subjectlevel features extracted from multimodal brain graphs to construct a population graph for gender classification. We show that while the extracted subject-level features can be directly used for classification, using these graph embeddings to construct a population graph further improves model performance. On the gender classification task, BrainGAT outperforms baseline models and existing multimodal modeling approaches, achieving an accuracy of 83.13% on the Human Connectome Project dataset. Salient connections highlighted by BrainGAT include connections between the inferior parietal and dorsolateral prefrontal areas of the cortex for females, while connections within the posterior cingulate cortex are highly salient for males. In sum, BrainGAT enables multimodal data to be modelled via population graphs in a parameter-efficient way. Clinical RelevanceSeveral neurological conditions exhibit significant differences across genders and multimodal studies on these diseases are increasingly prevalent. This work highlights gender differences of multimodal connectomes in neurotypical settings. These insights could help to separate multimodal disease biomarkers from fundamental gender differences.

neuroscience↗

Protein language models-assisted engineering of Uracil-N glycosylase enables programmable T-to-G and T-to-C base editing

Current base editors use DNA deamination enzymes, such as cytidine deaminase (CBE) or adenine deaminase (ABE), to facilitate transition nucleotide substitutions. Combining CBE or ABE with glycosylase enzymes, including CGBE and AYBE, can induce limited transversion mutations. Nonetheless, a critical demand remains for base editors capable of generating alternative mutation types, such as T>G corrections, which could address over 17% of monogenic SNVs responsible for human genetic diseases. In this study, we leveraged protein language models to engineer a uracil-N-glycosylase (UNG) variant with altered substrate specificities to thymines (eTDG). Notably, after only two rounds of testing fewer than 50 predicted variants, more than 50% exhibited a 1.5-11-fold enhancement in enzymatic activities, a success rate much greater than random mutagenesis. When eTDG was fused with Cas9 nickase without deaminases, it effectively induced programmable T to G or T to C substitutions and precisely corrected db/db diabetic mutation in mice (up to 55%). Our findings not only establish orthogonal strategies for developing novel base editors, but also demonstrate the capacities of protein language models for optimizing enzymes without extensive task-specific training data or laborious experimental procedures.

bioengineering↗

Adipokinetic hormone signaling mediates the fecundity of Diaphorina citri infected by Candidatus Liberibacter asiaticus

Diaphorina citri serves as the primary vector for Candidatus Liberibacter asiaticus (CLas), the bacterium associated with the severe Asian form of huanglongbing. CLas-positive D. citri are more fecund than their CLas-negative counterparts and require extra energy expenditure. Therefore, understanding the molecular mechanisms linking metabolism and reproduction is of particular importance. In this study, we found adipokinetic hormone (DcAKH) and its receptor (DcAKHR) were essential for increasing lipid metabolism and fecundity in response to CLas infection in D. citri. Knockdown of DcAKH and DcAKHR not only resulted in the accumulation of triacylglycerol and a decline of glycogen, but also significantly decreased fecundity and CLas titer in ovaries. Combined in vivo and in vitro experiments showed that miR-34 suppresses DcAKHR expression by binding to its 3 untranslated region, whilst overexpression of miR-34 resulted in a decline of DcAKHR expression and CLas titer in ovaries and caused defects that mimicked DcAKHR knockdown phenotypes. Additionally, knockdown of DcAKH and DcAKHR significantly reduced juvenile hormone (JH) titer and JH signaling pathway genes in fat bodies and ovaries, including the JH receptor, methoprene-tolerant (DcMet), and the transcription factor, Kruppel homolog 1 (DcKr-h1), that acts downstream of it, as well as the egg development related genes vitellogenin 1-like (DcVg-1-like), vitellogenin A1-like (DcVg-A1-like) and the vitellogenin receptor (DcVgR). As a result, CLas hijacks AKH/AKHR-miR-34-JH signaling to improve D. citri lipid metabolism and fecundity, while simultaneously increasing the replication of CLas, suggesting a mutualistic interaction between CLas and D. citri ovaries.

ecology↗

Bridging the 3D geometrical organisation of white matter pathways across anatomical length scales and species

We used diffusion MRI and x-ray synchrotron imaging on monkey and mice brains to examine the organisation of fibre pathways in white matter across anatomical scales. We compared the structure in the corpus callosum and crossing fibre regions and investigated the differences in cuprizone-induced demyelination mouse brains versus healthy controls. Our findings revealed common principles of fibre organisation that apply despite the varying patterns observed across species; small axonal fasciculi and major bundles formed laminar structures with varying angles, according to the characteristics of major pathways. Fasciculi exhibited non-straight paths around obstacles like blood vessels, comparable across the samples of varying fibre complexity and demyelination. Quantifications of fibre orientation distributions were consistent across anatomical length scales and modalities, whereas tissue anisotropy had a more complex relationship, both dependent on the field-of-view. Our study emphasises the need to balance field-of-view and voxel size when characterising white matter features across length scales.

neuroscience↗

Serum-deprivation response of ARPE-19 cells; expression patterns relevant to age-related macular degeneration.

ARPE-19 cells are derived from adult human retinal pigment epithelium (RPE). The response of these cells to the stress of serum deprivation mimics some important processes relevant to age-related macular degeneration (AMD). Here we extend the characterization of this response using RNASeq and EGSEA gene set analysis of ARPE-19 cells over nine days of serum deprivation. This experiment confirmed the up-regulation of cholesterol and lipid-associated pathways that increase cholesterol levels in these cells. The gene expression analysis also identified other pathways relevant to AMD progression. There were significant changes in extracellular matrix gene expression, notably a switch from expression of collagen IV, a key component of Bruchs membrane (part of the blood-retina barrier), to expression of a fibrosis-like collagen type I matrix. Changes in the expression profile of the extracellular matrix led to the discovery that amelotin is induced in AMD and is associated with the development of the calcium deposits seen in late-stage geographic atrophy. The transcriptional profiles of other pathways, including inflammation, complement, and coagulation, were also modified, consistent with immune response patterns seen in AMD. As previously noted, the cells resist apoptosis and autophagy but instead initiate a gene expression pattern characteristic of senescence, consistent with the maintenance of barrier function even as other aspects of RPE function are compromised. Other differentially regulated genes were identified that open new avenues for investigation. Our results suggest that ARPE-19 cells maintain significant stress responses characteristic of native RPE that are informative for AMD. As such, they provide a convenient system for discovery and for testing potential therapeutic interventions.

molecular biology↗

Microglia facilitate and stabilize the response to general anesthesia

General anesthesia leads to a loss of consciousness and an unarousable state in patients. Although general anesthetics are widely used in clinical practice, their underlying mechanisms remain elusive. The potential involvement of nonneuronal cells is unknown. Microglia are important immune cells in the central nervous system (CNS) that play critical roles in CNS function and dysfunction. We unintentionally observed delayed anesthesia induction and early anesthesia emergence in microglia-depleted mice. We found that microglial depletion differentially regulates neuronal activities by suppressing the neuronal network of anesthesia-activated brain regions and activating emergence-activated brain regions. Thus, microglia facilitate and stabilize the anesthesia status. This influence is not mediated by dendritic spine plasticity. Instead, it relies on the activation of microglial P2Y12 and subsequent calcium influx, which facilitates the general anesthesia response. Together, we elucidate the regulatory role of microglia in general anesthesia, extending our knowledge of how nonneuronal cells modulate neuronal activities.

neuroscience↗