bioRxiv Science⌕ Search

Biology subjects

Wu, Y.

Publications and source records attributed to Wu, Y..

At least 217 records · Page 12Linked to original sources

Disentangling Cephalopod Chromatophores Motor Units with Computer Vision

Cephalopod chromatophores are skin pigment organs that enable unmatched camouflage through rapid, flexible and neurally controlled deformation. Although their morphology is well known, the organization of their motor control is not entirely understood. Here, we combine high-resolution videography with a dedicated computer-vision pipeline (CHROMAS) to investigate chromatophore control and their likely innervation in Euprymna berryi and Sepia officinalis. By segmenting chromatophores into radial slices and analyzing anisotropic deformations, we applied dimensionality reduction (PCA) and source separation (ICA) to estimate the number and spatial influence of motor neurons responsible for the control of individual and groups of chromatophores. On average, four independent components were detected (suggesting innervation by four motor neurons), each forming contiguous petal-shaped domains rather than causing uniform expansion. Clustering thousands of components revealed motor units spanning multiple chromatophores, most involving fewer than 14 but occasionally spanning more widely. These motor units displayed a wide variety of geometries, ranging from compact local groups to elongated or fragmented structures; they often overlapped, with repeated co-innervation of chromatophore pairs occurring more often than expected by chance. Expansion was consistently faster and more stereotyped than relaxation, consistent with active contraction (corresponding to chromatophore expansion) and passive recoil (chromatophore contraction). Together, these results show that individual chromatophores are not singular or uniform pixels, but rather contrast elements that can be fractionated into smaller territories, themselves coordinated with those of other chromatophores. This geometry of neural control enables, among others, the generation of "virtual" chromatophores, i.e., functional groupings of adjacent chromatophore territories that act as single units, as well as that of noise in the distribution of pixel shapes.

neuroscience↗

Integrative spatial multi-omics reveals prognostic tumor niches in female genital tumors

Female genital tumors (FGTs), including ovarian, endometrial, and cervical cancers, pose a major global health challenge, yet their spatial and molecular determinants of progression and therapy resistance remain poorly understood. Here we present a large-scale integrative spatial and multi-omics atlas of FGTs, combining exome, transcriptome, methylome, and miRNA sequencing with high-resolution Visium HD spatial transcriptomics, profiling over 62 million cells from 100 tumors. We show that HPV-driven suppression of TGF{beta} signaling in cervical cancer disrupts myofibroblast (myCAF) formation and reshapes immune infiltration, while serous tumors exhibit extensive oncogene amplifications that activate MYC and PI3K pathways, linking chromosomal instability (CIN) to proliferative, immune-cold phenotypes. In high-grade serous ovarian cancer, we identify a previously unrecognized malignant domain, the Proliferating Core Desert (PCD) niche, defined by CIN-high epithelial enrichment, immune exclusion, stromal protection, and chemotherapy resistance, maintained through crosstalk with macrophages and fibroblasts. Finally, we develop POWER, a pathology foundation model that predicts PCD niche abundance from routine H&E slides, enabling robust stratification of prognosis and anti-angiogenic therapy response.

genomics↗

Anionic Lipid Trafficking and Cell Mechanics RegulateMembrane Electrical Potential in Non-Excitable Tissue Cells

1The membrane potential of eukaryotic cells, classically described by the Goldman-Hodgkin-Katz model, is conventionally attributed to the steady-state balance of transmembrane ionic fluxes. Here, we demonstrate that non-excitable cells maintain stable, spatially heterogeneous membrane voltage gradients. Using the ratiometric voltage indicator JEDI-2P-cyOFP1, we quantitatively map membrane potential in live cells and find that cellular protrusions are consistently depolarized, whereas lateral membrane regions are hyperpolarized. These voltage gradients strongly correlate with anisotropic distributions of anionic lipids, including phosphatidylserine (PS) and phosphatidylinositol 3,4,5-trisphosphate (PIP3). Perturbation of cytoskeletal integrity, the ion exchanger NHE1, or vesicular trafficking disrupts both voltage anisotropy and lipid polarization, revealing an uncharacterized electromechanical regulatory mechanism. Moreover, membrane potential dynamically responds to cell shape, substrate stiffness, external electric fields, and cell cycle progression. To account for these phenomena, we develop a quantitative model that integrates ionic fluxes and lipid charge distributions, thereby explaining the emergence of voltage gradients. This framework establishes that membrane potential is governed not solely by ionic currents but also by lipid dynamics and mechanical signaling. Collectively, these findings identify membrane voltage as a global integrator of electrochemical and mechanical cues in eukaryotic cells.

biophysics↗

Repurposed endogenous virus-like vesicles mediate dendritic cell long-range antigen presentation and T cell activation for enhanced cancer vaccination

Dendritic cells (DCs) release extracellular vesicles (DEVs) that amplify antigen presentation while incorporating patient-derived, rapidly evolving antigens. By enriching peptide-MHC and co-stimulatory ligands orders-of-magnitude above donor-cell levels, DEVs emerge as potent vesicle-vaccines, although efficacy remains limited by unclear mechanisms. We show that DCs repurpose viral components to generate endogenous virus-like vesicles (VLVs) that preferentially carry peptide-MHC and high-density co-stimulatory ligands, intensifying and extending antigen presentation. Upon antigen exposure, Arc partners with endogenous envelope proteins to assemble VLVs that directly engage T cells and trigger intrinsic adjuvanticity via viral mimicry. Arc-/- DEVs failed to prime antigen-specific T cell responses, whereas Arc overexpression with its 5'-UTR stem-loop shifted DEVs toward VLVs that trafficked to lymphoid organs, drove rapid CD4-assisted priming and durable CD8-biased memory, suppressed melanoma, and prolonged survival. These reveal a viral-mimicry mechanism enabling long-range immune activation and support Arc+ VLVs as an antigen-agnostic vaccine for cancer immunotherapy. HighlightsO_LIArc+ VLVs intensify and extend DC antigen presentation in vivo C_LIO_LIArc+ VLVs directly engage T cells and trigger viral-mimic adjuvanticity C_LIO_LIArc-/- DEVs fail to prime antigen-specific T cell responses C_LIO_LIEngineered Arc+ VLVs drive durable CD8-biased memory and tumor control C_LIO_LIArc+ VLV vaccination provides long-range and cross-tumor protection in vivo C_LI

bioengineering↗

TAp73 mediates anti-tumor immunity through regulation of lipid metabolism in the lung tumor microenvironment

While immunotherapy has become the standard of care for lung adenocarcinoma (LUAD) patients without actionable genomic alterations, only a subset of patients benefits from a long-lasting response to immunotherapy. Activation of p53-related signals has emerged as a potential mediator of the lung tumor microenvironment (TME). Given that mutant-p53 interacts with p73 extensively and TAp73-deficient mice develop LUAD, we engineered a mouse model with conditional deletion of TAp73 to understand the interactions of the p53 family in the TME and in metabolic pathways that impact anti-tumor immunity. We demonstrated that TAp73 exerts a tumor-suppressive role in KrasG12D-driven LUAD by regulating lipid metabolism in the TME. We identified a TAp73-driven transcriptional signature involving genes in the arachidonic acid metabolism pathway operational in tumor-associated macrophages that favors T-cell activation and thus anti-tumor immunity. Similar transcriptional changes are seen in macrophages from LUAD patients with p53 mutations and in association with response to immunotherapy. SIGNIFICANCEThere is a need to understand how the LUAD TME impacts patient response to immunotherapy. We identified a transcriptional program enacted by TAp73 in tumor alveolar macrophages that supports T-cell activation. Transcriptional and metabolomic data from LUAD patients supports the relevance of this program in response to immune checkpoint inhibition.

cancer biology↗

Accurate Probabilistic Reconstruction of Cell Lineage Trees from SNVs and CNAs with ScisTreeCNA

Cell lineage tree is a fundamental evolutionary model for single-cell evolution. Inference of cell lineage tree from noisy single-cell DNA data has been studied actively in recent years. Existing methods for cell lineage tree inference can be classified into two categories based on the type of genetic variations they work with: single-nucleotide variants (SNVs) or copy-number aberrations (CNAs). Due to various noises and uncertainties in the data, the existing methods are not fully satisfactory, in part because they only used one type of genetic variant. Single-cell DNA sequencing data with both SNVs and CNAs are becoming available. In principle, joint inference of cell lineage trees from both SNVs and CNAs may lead to more accurate results. However, there is a lack of rigorous models and efficient algorithms for such inference. In this paper, we present a new cell lineage tree inference method, called ScisTreeCNA, that jointly infers cell lineage trees from SNVs and CNAs. A key contribution of ScisTreeCNA is a novel probabilistic model for the joint evolution of SNVs and CNAs in single cell data. Based on this model, ScisTreeCNA implemented several efficient algorithms for accelerating probabilistic inference of cell lineage tree. Experiments on both simulated and real biological data show that ScisTreeCNA consistently outperforms existing methods in the accuracy of the inferred cell lineage trees. ScisTreeCNA is available at https://github.com/haotianzh/ScisTreeCNA.

bioinformatics↗

Two-photon characterisation of long-Stokes-shift dye ATTO 490LS for single-laser multicolour imaging

Long-Stokes-shift fluorophores enable high sensitivity and multiplexed imaging with single-wavelength excitation. Under single-photon illumination ATTO 490LS exhibits a 165-nm Stokes shift, but its two-photon properties remain uncharacterised. Emission and excitation spectral analyses of ATTO 490LS in ex vivo Drosophila melanogaster brains identified two-photon excitation sensitivity at 940 nm, with peak emission at 640 nm. We demonstrate successful duplexed imaging of ATTO 490LS alongside Alexa Fluor 488 using a single 920-nm fibre laser and dual photomultiplier tubes, enabling distinct measurement of red and green fluorescence signals. These findings establish ATTO 490LS as suitable for multicolour two-photon microscopy with single-laser systems.

neuroscience↗

Vectorial boundary representation of 3D layout in human visual cortex

Human spatial navigation relies on the brains ability to visually represent the 3D layout of the environment. To understand how the brain encodes the layout information, it is crucial to identify the key features of environmental layout and how they are processed in the human brain. The vector coding principle, which highlight the role of boundary distance and orientation, provides a theoretical framework supported by physiological evidence from rodents. In this study, we developed a reconstruction approach to quantitatively estimate 3D layout information from natural indoor scene images. This approach enabled analyses of fMRI data from the large-scale Natural Scenes Dataset (NSD) using vector-based models of 3D layout. To validate the NSD-based results and examine task-related dynamics, we further conducted fMRI and MEG experiments with navigation-related and non-navigational tasks. Controlling for low-, mid-, and high-level visual and semantic features of natural indoor scenes, we found a spatiotemporal dissociation between boundary distance and orientation representations in the human brain. Relative distance was encoded in the early visual cortex during early processing in a task-invariant manner, whereas orientation was represented in scene-selective higher visual areas during later processing and was modulated by navigation-related tasks. Importantly, task modulation manifested as feedback-induced enhancement of orientation coding in the early visual cortex. Together, these findings provide a novel perspective on how the human brain represents navigation-relevant information about the immediate surrounding environment, advancing our understanding of the neural mechanisms that link perception to action in spatial navigation.

neuroscience↗

Gut Microbiota-derived Adenosine Determines the Efficacy of Electroconvulsive Therapy for Depression

Electroconvulsive therapy (ECT) is a final procedure for major depressive disorders (MDD). However, the effectiveness of ECT in treating MDD patients varies. Here we identified gut microbiota as a potential restraining factor of ECT efficacy. By using a 5-day electroconvulsive shock (ECS) in depression mouse model of chronic restraint stress (CRS), it was observed that the antidepressant effect of ECS was suppressed after antibiotics (ABX)-induced microbiota dysbiosis, which also resulted in elevated c-Fos expression of CRH neurons in paraventricular nucleus of hypothalamus (PVN) and increased serum corticosterone levels after ECS. Metabolomic analysis revealed the critical involvement of microbiota associated purine metabolism, and the supplement of gut microbiota-derived adenosine was able to recover the antidepressant effect of ECS in ABX-treated CRS mouse model. Based on the neural tracing from colon to brain and the immunofluorescence staining, it was surmised a gut-brain axis originated from Adora1-expressing cells in colon mediate this biological process. Furthermore, adenosine supplement alleviated the further deterioration of post-ECS memory loss and impairment of synaptic plasticity induced by ABX-treatment as well. Our findings suggest a potential role of microbial adenosine metabolism in ECT efficacy determination and side effect protection, highlights potential application of adenosine supplement in antidepressant therapies of those depression patients with microbiota dysbiosis.

systems biology↗

CDR Conformation Aware Antibody Sequence Design with ConformAb

Antibody lead optimization methods seek to enhance a lead candidates therapeutic properties through targeted sequence mutation. However, the mutations introduced during this process can inadvertently induce structural changes that disrupt binding, particularly by altering CDR loop conformations which destabilize CDR-target binding interactions. To address this, we present ConformAb, a guided discrete diffusion model for designing antibody sequences that explicitly conform to the CDR canonical conformation of the lead. With seed sequences as the starting point, we show that our method is capable of generating 3- 5x better binders that conform to the same CDR backbone structure in a one-shot design setup, and in some cases, binders with better affinity than seed repertoire picks without any target-specific data included in training. Across the targets tested, ConformAb demonstrated binding rates ranging from 15 -60% in wet lab experiments, a result obtained using fewer than 100 designs for each target. ConformAb offers a unique one-shot approach for antibody lead optimization in data-scarce scenarios where experimental/repertoire data cannot be leveraged for model training.

biophysics↗

Automation of high-throughput workflow for arrayed CRISPR activation library screening

CRISPR-mediated gene activation (CRISPRa) is among the most efficient and reliable strategies for mimicking sustained activation of endogenous promoters and their corresponding genes at physiological levels. By leveraging guide-RNA (gRNA) library design, CRISPRa screens can be applied on a whole-genome scale and are compatible with both arrayed and pooled formats, depending on assay requirements. Compared with conventional arrayed CRISPRa libraries that use single or dual gRNAs and often require multiple gRNA candidates per target, a recently developed CRISPRa library (termed T. gonfio) incorporates four tandem gRNAs per lentivector per target, thereby reducing library complexity and representing the smallest arrayed genome-wide CRISPRa library. To streamline genome-wide arrayed CRISPRa screening, this study developed a high-throughput automated workflow using the Biomek i7 Hybrid liquid-handling platform, integrated with multiple peripheral instruments. The workflow comprises three pipelines: lentiviral library transduction, cell library passaging, and assay processing. These pipelines together establish and maintain the transduced cell library for extended screening times. This enables assay processing at desired extended time points and improves the likelihood of identifying phenotypes that require longer time to develop, making the workflow suitable even for rapidly proliferating cell models. In a pilot arrayed screen using a T. gonfio mini-library targeting kinases and phosphatases, activation of the EPHA2 receptor promoter induced a growth reduction phenotype in the HEK293 cell model. This phenotype was recapitulated in a parallel pooled CRISPRa screen using the same mini-library and further validated in a co-culture assay.

cancer biology↗

A dimerization-activated proximity labeling system for direct characterization of cadherin cis interactions

E-cadherins (Ecads) are essential transmembrane cell-cell adhesion proteins that mediate epithelial tissue formation and maintenance. Robust adhesion requires cis dimerization between neighboring Ecads on the cell surface and previous structural and biophysical studies have proposed conflicting models on the role of specific and nonspecific interactions in mediating cis dimerization. However, since these studies were carried out with isolated Ecad extracellular regions in cell-free systems, it is unknown if specific and nonspecific cis binding modes also occur with transmembrane Ecads in live cells, and if specific and nonspecific cis dimers recruit different sets of cytoplasmic proteins to Ecad junctions. To directly address these knowledge gaps, we developed a Dimerization Activated TuboID (DAT) proximity labeling system that reports on different modes of Ecad cis binding and their corresponding proteomes. Using DAT, fluorescence measurements, diffusion-reaction simulations, and adhesion assays, we demonstrate that Ecads in live cells form cis dimers via both specific and non-specific interactions and that cis dimerization does not require either prior trans contacts or an intact actin cytoskeleton. However, we show that the loss of specific cis interactions results in increased junctional instability and Ecad mobility, which leads to dysregulated peripheral protein interactions without affecting recruitment of core junctional proteins. Our study provides key mechanistic insights on cadherin cis interactions and also presents a toolkit that can be used to study a broad range of protein cis dimers in live cells.

biophysics↗

The CENP-A chaperone complex spatially organizes centromeres

Centromeres, defined by CENP-A-containing nucleosomes, direct the assembly of kinetochores for spindle attachment. In mitosis, CENP-A and the constitutive centromere-associated network (CCAN) of the inner kinetochore are arranged into bipartite subdomains within clearings of chromatin. However, it remains unclear whether any of these features exist before mitosis. We show that in interphase, CENP-A and the CCAN assemble [~]200-300 nm shell-like structures that enclose a chromatin-poor central cavity. Strikingly, this cavity is occupied by the interphase-specific CENP-A chaperone complex, which promotes CENP-A assembly once per cell cycle. However, chaperone presence, but not CENP-A incorporation, is required to generate both the shell architecture and the chromatin clearing. The CCAN scaffold CENP-C, which links CENP-A nucleosomes to the chaperone complex, exhibits radial organization spanning the entire structure and is essential for its formation. These data uncover a previously unrecognized structural role for the CENP-A chaperone machinery in establishing interphase centromere architecture and suggest a mechanism by which this machinery configures centromeres for faithful kinetochore assembly and genome stability.

cell biology↗

Morphological Identification of Ticks in district Swabi, Mardan, and Charsadda

Ticks are ectoparasitic arthropods that play a significant role in transmitting pathogens to humans and animals. This study aimed to address the research gap in understanding the morphological diversity and distribution of tick species in Swabi, Mardan, and Charsadda districts of Pakistan, where tick-borne diseases are prevalent but poorly documented. The primary objectives were to identify tick species, document their morphological characteristics, and map their distribution patterns across different habitats. Field surveys were conducted over nine months, collecting tick specimens from forests, grasslands, and residential areas. Specimens were preserved and analyzed using stereo-zoom microscopy and taxonomic keys for accurate classification. Key findings revealed a diverse tick fauna, including hard ticks (Ixodidae), with variations in body size, colour patterns, capitulum shape, and scutum features. Some species were widely distributed across all three districts, while others exhibited localized patterns. The study provides the first comprehensive morphological identification of tick species in these regions, highlighting their potential role in disease transmission. The implications of this research are significant for public health and disease control. The data can inform targeted interventions, enhance disease surveillance programs, and support the development of preventive measures to mitigate tick-borne diseases. By contributing to tick taxonomy and epidemiology, this study lays the groundwork for protecting public health in the study regions and beyond. This study addresses the lack of data on tick diversity in high-prevalence regions of Pakistan, providing critical insights for disease control and public health strategies. Limited information exists on the morphological diversity and distribution of tick species in Swabi, Mardan, and Charsadda districts. To identify tick species, document morphological characteristics, and map their distribution patterns in the study areas. Field surveys, specimen collection, stereo-zoom microscopy, and taxonomic classification were employed over nine months. Diverse tick fauna was identified, including hard ticks, with variations in morphology and distribution. Some species were widespread, while others were localized, highlighting potential disease transmission risks. The findings support targeted interventions, disease surveillance, and preventive measures, contributing to public health protection and tick-borne disease control in the region.

zoology↗

Bronsted-basic small molecules activate GTP hydrolysis in Ras Q61 mutants

The RAS oncogenes (KRAS, HRAS, NRAS) are among the most frequently mutated genes in human cancer, affecting over three million patients annually. Therapeutic development has largely focused on inhibitors for KRAS codon 12 mutations (G12C/D/V/S/R) which are key drivers in lung, colorectal, and pancreatic cancers. In contrast, mutant-selective inhibitors for Q61 variants remain elusive. A common mechanistic feature of G12 and Q61 mutants is the impaired hydrolysis of GTP, which traps Ras in its active, signaling-competent state. We envisioned that an alternative therapeutic strategy - reactivation of GTP hydrolysis - could address this shared oncogenic mechanism. Here we report small molecules that accelerate GTP hydrolysis in K-Ras Q61 mutants. These compounds compensate for the loss of the catalytic residue Gln61 by introducing a general base into the active site, selectively enhancing hydrolysis of K-Ras Q61X (X = H, L, K, R) mutants by up to 20-fold while sparing the wild-type protein. In mutant cancer cell lines, these compounds reduce GTP-bound Ras levels and suppress downstream signaling. We show that the chemical design principles are generalizable to other Ras isoforms. This work establishes a mechanistic foundation for small-molecule "GTPase activators" and offers a new paradigm for targeting Ras-driven cancers.

cancer biology↗

Delivery of collagen-encoding mRNA to the skin for cosmetic applications

Collagens, the predominant structural proteins in mammalian, maintain tissue integrity through its unique triple-helical conformation. Traditionally, cosmetic collagens have been administered as hydrolyzed peptides derived from animal sources, which exhibit poor bioavailability and functional efficacy due to limited skin penetration and disrupted tertiary/quaternary structures. To overcome these limitations, we developed a novel system for in vivo collagen expression. This system utilizes the topical application of in vitro synthesized, AI-designed mRNAs encoding types I, III, and XVII collagens to improve human skin condition. Significant upregulation of target collagen expression was observed in dermal fibroblasts, leading to improved skin condition through in situ assembly of collagens in natural conformation.

bioengineering↗

The O-glycosyltransferase SECRET AGENT Participates in Abscisic Acid-Induced Microtubule Remodeling and Stomatal Closure in Arabidopsis thaliana

Secret Agent (SEC) encodes the major O-GlcNAc transferase in Arabidopsis thaliana and has been implicated in stress and signaling pathways, but its role in stomatal regulation remains unknown. In this study, we investigated the function of SEC in abscisic acid (ABA)-induced stomatal closure and drought responses. Loss of SEC function in the sec-5 mutant delayed stomatal closure and increased water loss under drought, whereas SEC overexpression enhanced stomatal responsiveness and drought tolerance. Pharmacological assays revealed that sec-5 was less sensitive to microtubule-stabilizing and -disrupting drugs during ABA-induced stomatal closing, consistent with a defect in cytoskeletal dynamics. Confocal imaging and quantitative analysis of microtubule rearrangements showed that SEC loss-of-function mutation retarded microtubule reorganization in response to ABA, with abnormal microtubule bundling and density. Mechanistically, SEC physically interacted with -tubulin 4 (TUA4) in both yeast two-hybrid and bimolecular fluorescence complementation assays, suggesting tubulin as a potential substrate of SEC-modified O-GlcNAcylation. Together, these findings establish SEC as a key regulator of ABA-induced microtubule remodeling in guard cells, thereby linking O-GlcNAcylation to stomatal regulation and drought tolerance.

plant biology↗

Using the simple telegraph model to decipher transcriptional burst regulation across genome-wide data

Gene transcription is a stochastic bursting process, with burst frequency and burst size as core parameters. Deciphering its genome-wide regulation is challenging, as complex models (capturing detailed biology) are impractical for large-scale use due to unstable inference and high computation. We proposed a simple telegraph model-based framework to analyze genome-wide scRNA-seq and smFISH datasets, addressing these limitations. When sample size [≥] 500 and burst parameter change [≥] 3-fold, its inferred burst frequency- and size-dominated variations reliably proxy true regulation. Analyses across mouse cells (CAST/C57 alleles, fibroblasts vs. embryonic stem cells) and healthy/hypertrophic cardiomyopathy (HCM) human heart tissues revealed key rules: 1) Burst frequency- or size-dominated regulation was primary (over 70% of variable genes), with more bursty-regulated genes in HCM; 2) TATA-initiator synergy (enhancing burst size-dominated regulation) was lost in HCM; 3) Burst frequency-dominated genes enriched in genome stability/cell cycle/apoptosis (via TFs like Foxo4/Mcm2), while burst size-dominated ones in signaling/metabolism/proteostasis (via TFs like Zfp322a/Smchd1/Ppargc1a), and their interdependent dysregulation accelerated HCM. This study establishes the simple telegraph model as a scalable framework linking transcriptional burst dynamics to cell fate and pathology.

molecular biology↗