Biology subjects

Yu, Y.

Publications and source records attributed to Yu, Y..

At least 199 records · Page 11Linked to original sources

bioRxiv2024

TrimNN: Characterizing cellular community motifs for studying multicellular topological organization in complex tissues

The spatial organization of cells plays a pivotal role in shaping tissue functions and phenotypes in various biological systems and diseased microenvironments. However, the topological principles governing interactions among cell types within spatial patterns remain poorly understood. Here, we present the Triangulation Cellular Community Motif Neural Network (TrimNN), a graph-based deep learning framework designed to identify conserved spatial cell organization patterns, termed Cellular Community (CC) motifs, from spatial transcriptomics and proteomics data. TrimNN employs a semi-divide-and-conquer approach to efficiently detect over-represented topological motifs of varying sizes in a triangulated space. By uncovering CC motifs, TrimNN reveals key associations between spatially distributed cell-type patterns and diverse phenotypes. These insights provide a foundation for understanding biological and disease mechanisms and offer potential biomarkers for diagnosis and therapeutic interventions.

bioinformatics↗

bioRxiv2024

Genomic and transcriptomic profiling of high-risk bladder cancer reveals diverse molecular and microenvironment ecosystems

Despite surgical resection, rigorous endoscopic surveillance, and immunotherapy with the Bacillus Calmette-Guerin (BCG) vaccine, 30% of high-risk bladder cancers recur, and 10% result in fatal outcomes within two years of diagnosis. The global shortage of BCG underscores the urgent need for alternative or complementary therapeutic strategies. To address this, we integrated transcriptomic profiling and targeted genomic sequencing to identify four consensus intrinsic subtypes of bladder cancer. Initially derived from bulk RNA profiling, these subtypes were further validated at the cellular and tissue-compartment levels using single-cell RNA sequencing and spatial transcriptomics. Notably, we identified a subtype of inflamed tumors with enhanced endogenous retroelement expression and increased commensal bacterial presence, which showed the highest responsiveness to BCG therapy. Additionally, we developed a machine learning-based model incorporating composite molecular features to predict recurrence risk, achieving a high accuracy (AUC = 0.90). Our findings establish a molecular precision framework for bladder cancer and nominate novel therapeutic targets to reduce reliance on BCG immunotherapy.

cancer biology↗

bioRxiv2024

HCN1 channels in GABAergic amygdalar neurons underpin male-biased aggressive behaviors

Aggression behaviors typically vary between sexes, but the molecular mechanisms driving these disparities in neural coding are unclear. We found that aggression selectively activates GABAergic neurons in the posterior substantia innominata (pSI), an extend amygdala region critical for aggressive behaviors in both sexes of mice, with males exhibiting higher neuronal activity during the attack. Utilizing single-nucleus RNA sequencing, we characterized the diverse molecular landscape of pSI neurons, revealing significant differences in ion channels and hormone regulator genes that may underpin sex-specific aggression. Male GABAergic pSI neurons exhibited remarkable hyperexcitability due to increased Ih currents. Strikingly, modulating HCN1 expression not only adjusted this hyperexcitability but also influenced sexual dimorphism in aggression: silencing HCN1 in the GABAergic pSI neurons reduced male aggression, while its overexpression markedly heightened aggression in females. Furthermore, testosterone was shown to intensify aggression by upregulating HCN1 and remodeling pSI circuits. These findings provide detailed sex-specific molecular mechanisms underlying social behaviors.

neuroscience↗

bioRxiv2024

Ultra-Efficient Integration of Gene Libraries onto Yeast Cytosolic Plasmids

Efficient methods for diversifying genes of interest (GOIs) are essential in protein engineering. For example, OrthoRep, a yeast-based orthogonal DNA replication system that achieves the rapid in vivo diversification of GOIs encoded on a cytosolic plasmid (p1), has been successfully used to drive numerous protein engineering campaigns. However, OrthoRep-based GOI evolution has almost always started from single GOI sequences, limiting the number of locations on a fitness landscape from where evolutionary search begins. Here, we present a simple approach for the high-efficiency integration of GOI libraries onto OrthoRep. By leveraging integrases, we demonstrate recombination of donor DNA onto the cytosolic p1 plasmid at exceptionally high transformation efficiencies, even surpassing the transformation efficiency of standard circular plasmids into yeast. We demonstrate our methods utility through the straightforward construction of mock nanobody libraries encoded on OrthoRep, from which rare binders were reliably enriched. Overall, integrase-assisted manipulation of yeast cytosolic plasmids should enhance the versatility of OrthoRep in continuous evolution experiments and support the routine construction of large GOI libraries in yeast in general.

synthetic biology↗

bioRxiv2024

Defining the parameters for sorting of different RNA cargo into Extracellular vesicles

Extracellular vesicles (EVs) are small particles that are released by cells and mediate cell-cell communication by transferring bioactive molecules. RNA cargo of EVs, including coding and non-coding RNAs, can change the behavior of recipient cells, affecting processes like gene expression, proliferation, and apoptosis. Circular RNAs (CircRNA) are a newly appreciated class of regulatory RNAs that are stable, resistant to degradation and have been shown to be enriched in EVs. They play key roles in gene regulation and are also emerging as promising biomarkers for disease diagnosis. While microRNAs (miRNAs) are the most well studied RNA cargo of EVs, very little is known about the mechanisms of enrichment of circRNAs as well as long linear RNAs. Here, we take a comprehensive genome-wide approach to investigate the role of GC%, size, exon count, structuredness and coding potential, in the sorting and enrichment of circular and long linear RNAs into EVs. We found that size and structuredness had a significant role in enriching RNAs into EVs which was consistent across all classes of RNAs. Furthermore, we found that structuredness could explain the relative enrichment of circRNAs over their linear counterparts. These results were validated on existing public databases of circular and linear RNAs in EVs. By identifying and analyzing these factors, we aim to better understand the complex mechanisms behind EV-mediated RNA transfer and its impact on cell communication in both health and disease. This mechanistic understanding of RNA enrichment in EVs is crucial for engineering EVs with selective RNA cargo.

cell biology↗

bioRxiv2024

Naturally-occurring, strain-specific defects in the retraction of Acinetobacter baumannii type IV pili promote biofilm formation

Type IV pili are helical filaments composed of protein subunits which are produced by numerous taxa of bacteria, including Acinetobacter. Type IV pili are extended out from the cell by extension enzyme complexes, which extract subunits from the membrane and insert them into the base of the filament, but can also be retracted by reverse rotation catalyzed by a retraction enzyme. Type IV pili have diverse functions, and some (twitching motility, DNA-uptake) require retraction while others (host adhesion, bacterial aggregation) do not. Acinetobacter bacteria, including International Clone I (IC-I) and International Clone II (IC-II) strains, show variable phenotypes in assays of type IV pilus-dependent functions. We show this variation is the result of variable efficiency in pilus retraction between pilus subtypes, and from that, a differential balance between retraction-dependent and retraction-independent functions. We define type IV pilus subtypes based on the sequence of the major subunit, PilA. In both naturally-occurring pilA variants from the IC-I and IC-II groups and isogenic strains complemented with IC-I or IC-II pilA, the IC-I pilus subtype promotes greater twitching motility and DNA-uptake while the IC-II pilus subtype promotes biofilm formation while showing reduced capacity for DNA-uptake and twitching motility, similar to a retraction-deficient mutant and consistent with the hypothesis that pilus retraction of the IC-II pilus is naturally deficient. Testing the hypothesis that this defect in retraction was sufficient to increase the level of piliation on the cell surface, we compared the yields of T4P sheared from the cell surface and found that in an isogenic background, complementation with IC-II pilA results in greater levels of surface PilA per cell than equivalent complementation with an IC-I pilA gene.

microbiology↗

bioRxiv2024

A regulator controls both DNA damage response and anti-phage defense networks in Moraxellaceae

DNA damage chemicals, including many antibiotics, often induce prophage induction and phage outbreaks in microbial communities, a major threat to bacterial survival. Moraxellaceae contains clinically highly relevant strains with outstanding antibiotic and radio resistance, yet their cellular-level regulation in DNA damage response and anti-phage defense is largely unknown. Here, we identified a WYL family protein that had replaced the ubiquitous SOS system in evolution and directly regulated a transcriptional network of both DNA repair genes and anti-phage defense genes under DNA damage stress. This study depicts a mechanism that how bacteria maintain immunity to phages without compromising on antibiotic resistance, and sheds light on controlling the resistance of Moraxellaceae strains in clinical practice.

microbiology↗

bioRxiv2024

Annotating CryoET Volumes: A Machine Learning Challenge

Cryo-electron tomography (cryoET) has emerged as a powerful structural biology tool for understanding protein complexes in their native cellular environments. Presently, 3D volumes of cellular environments can be acquired in the thousands in a few days where each volume provides a rich and complex cellular landscape. Despite numerous innovations, localizing and identifying the vast majority of protein species in these volumes remains prohibitively difficult. Machine learning based methods provide an opportunity to automate the process of labeling and annotating cryoET volumes. Due to current bottlenecks in the annotation process, and a lack of large standardized datasets, training datasets for machine learning algorithms have been scarce. Here, we present a defined "phantom" sample, along with "ground truth" annotations, that will be the basis of a machine learning challenge to bring cryoET and ML experts together and spur creativity to address this annotation problem. We have also set up a cryoET data portal that provides additional diverse sets of annotated 3D volumes from cryoET experts across the world for the machine learning challenge.

cell biology↗

bioRxiv2024

Non-gonadal PIWI protein, Aubergine, regulates regenerative stem cell proliferation and tumourigenesis in the Drosophila adult intestine.

The PIWI-interacting RNA (piRNA) biosynthesis pathway is best studied for its role suppressing Drosophila germline transposable elements. Piwi, the founding member of the pathway, is involved in adult intestinal stem cell (ISC) homeostasis. Whether a broader role of the PIWI pathway exists in the intestine, remains unknown. Here, we characterise a role of the PIWI family protein Aubergine (Aub) in ISCs. While dispensable for basal ISC self-renewal, upregulation of Aub by damage-induced reactive oxygen species drives regenerative ISC proliferation through increased protein synthesis, including translation of ISC factors Myc and Sox21a. Unexpectedly, such roles of Aub in ISCs appear uncoupled from its piRNA regulatory function. Additionally, Aub and mammalian PIWIL1, mediate tumorigenic intestinal growth in Drosophila and human organoids, respectively. Our results reveal regulated protein translation as a fundamental aspect of regenerative ISC function and discover a central role of Aub in such process.

developmental biology↗

bioRxiv2024

Learning allosteric interactions in Gα proteins from molecular dynamics simulations

G is a key subunit of heterotrimeric guanine-nucleotide-binding regulatory proteins, yet its conformational dynamics are not fully understood. In this study, we developed a Transformer-based graph neural network framework, Dynamic-Mixed Transformer (DMFormer), to investigate conformational dynamics of Go. DMFormer achieved an AUC of 0.75 on the training set, demonstrating robustness in distinguishing active and inactive states. The interpretability of the model was enhanced using integrated gradients, identifying the Switch II as a critical motif in stabilizing the active state and revealing distinct movement patterns between GTPase and -Helix domains. Our findings suggest that the conformational rigidity of the Q205L mutant in the Switch II segment leads to persistent activation. Overall, our study showcases DMFormer as an effective tool for analyzing protein conformational dynamics, offering valuable insights into activation mechanisms of G protein.

biophysics↗

bioRxiv2024

An IFN-STAT1-CYBB Axis Defines Protective Plasmacytoid DC to Neutrophil Crosstalk During Aspergillus fumigatus Infection.

Aspergillus fumigatus is the most common cause of invasive aspergillosis (IA), a devastating infection in immunocompromised patients. Plasmacytoid dendritic cells (pDCs) regulate host defense against IA by enhancing neutrophil antifungal properties in the lung. Here, we define the pDC activation trajectory during A. fumigatus infection and the molecular events that underlie the protective pDC - neutrophil crosstalk. Fungus-induced pDC activation begins after bone marrow egress and results in pDC-dependent regulation of lung type I and type III IFN levels. These pDC-derived products act on type I and type III IFN receptor-expressing neutrophils and control neutrophil fungicidal activity and reactive oxygen species production via STAT1 signaling in a cell-intrinsic manner. Mechanistically, neutrophil STAT1 signaling regulates the transcription and expression of Cybb, which encodes one of five NADPH oxidase subunits. Thus, pDCs regulate neutrophil-dependent immunity against inhaled molds by controlling the local expression of a subunit required for NADPH oxidase assembly and activity in the lung. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/620079v2_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1394ccforg.highwire.dtl.DTLVardef@e1bb13org.highwire.dtl.DTLVardef@1c0f991org.highwire.dtl.DTLVardef@40d5db_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Enhanced immune evasion of SARS-CoV-2 KP.3.1.1 and XEC through NTD glycosylation

KP.3.1.1 has surpassed KP.3 to become the new globally dominant strain, while XEC, a recombinant variant of KS.1.1/KP.3.3, is rapidly expanding across Europe and North America. Notably, both variants carry mutations, S31del of KP.3.1.1 and T22N of XEC, that could introduce new N-linked glycans on the Spike N-terminal domain (NTD), emphasizing the urgent need to assess their potential changes in viral characteristics. Here, we found that both KP.3.1.1 and XEC maintained the high ACE2-Spike binding affinity and pseudovirus infectivity of KP.3. Importantly, compared to KP.3, KP.3.1.1, and especially XEC, could further evade the neutralizing antibodies in convalescent plasma, even those elicited by KP.2-like breakthrough infections. Interestingly, both variants demonstrated increased resistance against monoclonal neutralizing antibodies targeting various epitopes on the receptor-binding domain (RBD). These suggest that the additional NTD glycosylation of KP.3.1.1 and XEC could enhance immune evasion via allosteric effects, and supports the future prevalence of XEC.

immunology↗

bioRxiv2024

Parkinsonism disrupts neuronal modulation in the pre-supplementary motor area during movement preparation

Multiple studies suggest that Parkinsons disease (PD) is associated with changes in neuronal activity throughout the basal ganglia-thalamocortical motor circuit. There are limited electrophysiological data, however, describing how parkinsonism impacts neuronal activity in the pre-supplementary motor area (pre-SMA), an area in medial frontal cortex involved in movement planning and motor control. In this study, single unit activity was recorded in the pre-SMA of two non-human primates during a visually cued reaching task in both the naive and parkinsonian state using the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model of parkinsonism. In the naive state neuronal discharge rates were dynamically modulated prior to the presentation of the instructional go-cue. In a subset of these modulated cells, the magnitude of modulation correlated linearly with reaction time (RT). In the parkinsonian state, however, modulation of discharge rates in the pre-SMA was disrupted and the predictive encoding of RT was significantly diminished. These findings add to our understanding of the role of pre-SMA in motor behavior and suggest that disrupted encoding in this cortical area contributes to the alteration of early preparatory and pre-movement processes that are present in Parkinsons disease. SIGNIFICANCE STATEMENTGoal-directed movements, such as reaching for an object, necessitate temporal preparation and organization of information processing within the basal ganglia-thalamocortical motor network. Impaired movement in people with Parkinsons disease is thought to be the result of pathophysiological activity disrupting information flow within this network. This work provides neurophysiological evidence linking altered motor preplanning processes encoded in pre-supplementary motor area (pre-SMA) neuronal firing to the pathogenesis of motor disturbances in parkinsonism.

neuroscience↗

bioRxiv2024

Generalizability of Normative Models of Brain Morphometry Across Distinct Ethnoracial Groups

Normative modeling of brain morphometric data can inform about the clinical significance of deviations from typical patterns in brain structure. Their usefulness, however, is dependent on their applicability to diverse ethnoracial groups. With this in mind, we developed age- and sex-specific normative models for cortical thickness, surface area, and subcortical volumes using brain scans from 37,407 healthy individuals from a diverse international sample. Here we demonstrate the validity of these models in diverse and distinct populations. Specifically, we tested these pre-trained models on independent samples of healthy individuals that either self-identified as Black, South Asian, East Asian Chinese, East Asian Japanese, or we categorized as African, Admixed American, East Asian, and European based on their genetic ancestry. Regardless of ethnoracial definition, the performance of the pretrained models in these samples was exceptionally high; the relative mean absolute error for each regional brain morphometry measure was less than 10% across all the distinct ethnoracial groups. These findings affirm the broad applicability of our models, ensuring that brain morphometry assessments using these models are accurate and reliable for individuals regardless of background. This broad applicability has significant implications for advancing personalized medicine and improving health outcomes in diverse populations.

bioinformatics↗

bioRxiv2024

Coma pattern-based autofocusing unlocks superior performance in unravelling single-cell dynamics during bacterial cold shock response

Imaging-based single-cell physiological profiling holds great potential for uncovering fundamental bacterial cold shock response (CSR) mechanisms, but its application is impeded by severe focus drift during rapid temperature downshifts required for CSR induction. Here, we introduce LUNA (Locking Under Nanoscale Accuracy), an innovative autofocusing method that leverages the coma pattern of detection light to characterize focus drift. LUNA improves the focusing precision down to 3 nm and extends the focusing range to at least 40 times the objective depth-of-focus. These advancements enable us to investigate the complete dynamics of bacterial single-cell CSR, revealing continuous cellular growth and division. We resolve a three-phase adaptation process characterized by distinct growth deceleration dynamics, and show that bacterial cells maintain robust size regulation and coordinate uniform adaptation to cold shock through synchronized growth and elapsed cycles. Notably, a model based on scattering theory reconciles the paradox between the growth lag of batch culture and continuous single-cell growth. These findings fundamentally transform our understanding of bacterial CSR and highlight LUNAs excellent potential for expanding state-of-the-art research in biology.

microbiology↗

bioRxiv2024

Wheat stripe rust resistance gene Yr9, derived from rye, is a CC-NBS-LRR gene in a highly conserved NLR cluster

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a significant threat to global wheat production. Genetic resistance plays a crucial role in controlling this disease. Among wheat breeding innovations, the wheat-rye 1BL.1RS translocations are notable for introducing alien genetic diversity, partly due to the presence of the stripe rust resistance gene Yr9 on 1RS. To clone Yr9, we first identified four Pst-susceptible mutants from Lumai 15, which carries the 1BL.1RS translocation and Yr9. Using these mutants, we performed Sequencing Trait-Associated Mutations (STAM). A single candidate gene, YrChr1B, was identified within the Yr9 locus and later confirmed as Yr9 through genetic complementation and gene editing. The Yr9 gene encodes a coiled-coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR or NLR) protein and is part of a 14-member NLR gene cluster. This cluster is conserved among Triticeae species and is an ortholog of the barley Mla locus. Cloning Yr9 expands the genetic resources available for molecular wheat breeding aimed at durable and broad-spectrum disease resistance.

plant biology↗

bioRxiv2024

How to select the best zero-shot model for the viral proteins?

Predicting the fitness of viral proteins holds notable implications for understanding viral evolution, advancing fundamental biological research, and informing drug discovery. However, the considerable variability and evolution of viral proteins make predicting mutant fitness a major challenge. This study introduces the ProPEC, a Perplexity-based Ensemble Model, aimed at improving the performance of zero-shot predictions for protein fitness across diverse viral datasets. We selected five representative pretrained language models (PLMs) as base models. ProPEC, which integrates perplexity-weighted scores from these PLMs with GEMME, demonstrates superior performance compared to individual models. Through parameter sensitivity analysis, we highlight the robustness of perplexity-based model selection in ProPEC. Additionally, a case study on T7 RNA polymerase activity dataset underscores ProPECs predictive capabilities. These findings suggest that ProPEC offers an effective approach for advancing viral protein fitness prediction, providing valuable insights for virology research and therapeutic development. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/616860v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@30be8forg.highwire.dtl.DTLVardef@2ebf35org.highwire.dtl.DTLVardef@10b517eorg.highwire.dtl.DTLVardef@134681_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Nanocluster-Mediated Signaling Crosstalk between FcγR and TLR4 in Macrophage Inflammatory Responses

Receptor crosstalk, the interaction between different receptors to modulate signaling, is crucial for fine-tuning the inflammatory responses of innate immune cells. Although the synergistic crosstalk between Toll-like receptor (TLR)4 and Fc gamma receptor (Fc{gamma}R) is well documented, the detailed mechanism underlying this synergy remains unclear. In this study, we addressed this knowledge gap by imaging the molecular organization of TLR4 and Fc{gamma}R on the macrophage cell surface and correlating it with their synergistic co-activation using ligands functionalized on lipid bilayers. We confirmed that co-activation of TLR4 and Fc{gamma}R enhances whole-cell pro-inflammatory responses and tyrosine phosphorylation at the receptor level. Super-resolution microscopy revealed that TLR4 and Fc{gamma}R each form discrete nanoclusters after ligand stimulation, and their synergistic co-activation significantly increases both the size and spatial overlap of these nanoclusters, leading to amplified immune signaling. Contrary to previous assumptions that TLR4 and Fc{gamma}R form heterodimers during their crosstalk, our results emphasize the critical role of receptor nanocluster interactions in modulating innate immune responses. Additionally, these findings align with similar receptor interaction mechanisms that we previously reported in other receptor pairs, such as Dectin-1/TLR2 and Fc{gamma}R/TLR2, suggesting that nanocluster interactions may represent a predominant mechanism governing crosstalk between TLRs and ITAM-containing receptors.

biophysics↗