Biology subjects

Wu, J.

Publications and source records attributed to Wu, J..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Vitreous Inflammation as an Early Indicator of Retinal Ganglion Cell Loss Following Acute Optic Nerve Injury in Mice

Retinal ganglion cell (RGC) degeneration in optic neuropathies is often preceded by neuroinflammatory changes, yet the earliest in vivo indicators of this process remain poorly defined. Here, we identified vitreous hyperreflective foci (VHRFs) by visible-light optical coherence tomography (vis-OCT) as an early inflammatory signature of RGC injury. Longitudinal vis-OCT imaging after optic nerve crush (ONC) revealed that VHRFs emerged as early as 6 hours post-injury and peaked before the significant RGC loss. Confocal analysis showed that these VHRFs corresponded to activated amoeboid microglia undergoing vertical migration from the outer to inner retina and horizontal movement toward the optic nerve head area. Similar amoeboid microglia were also observed in the anterior segment, suggesting a global ocular inflammatory response to the ONC injury. RNAscope in situ hybridization further demonstrated elevated IL-1{beta} expression in vitreous amoeboid microglia. Moreover, pharmacological blockade of IL-1 signaling with an IL-1 receptor antagonist significantly reduced VHRFs, suppressed microglial migration, and delayed RGC loss. Taken together, our findings identify VHRFs as a previously unrecognized early danger signal for RGC degeneration and highlight IL-1-mediated inflammation as a tractable early therapeutic target for preventing RGC degeneration and vision loss. Graphical Overview O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/694725v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1598c4aorg.highwire.dtl.DTLVardef@9637borg.highwire.dtl.DTLVardef@623bf4org.highwire.dtl.DTLVardef@14e21ce_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

DINOcell: Learning Generalizable Perturbation Effects through Self-Distillation

AO_SCPLOWBSTRACTC_SCPLOWPredicting cellular responses to therapeutics is a promising approach for novel target discovery. However, state-of-the-art computational models designed to predict perturbation effects struggle to generalize and outperform simple baselines. We present DINOcell, a weakly supervised framework that adapts self-distillation to single-cell transcriptomics for predicting perturbation effects. We demonstrate that DINOcell outperforms baselines in predicting the effects of single gene perturbations. Furthermore, DINOcell accurately predicts non-additive effects of combination perturbations, indicating its capacity to model complex genetic interactions. Finally, we show that DINOcell learns representations that capture biological signals and is a promising, generalizable approach for in silico perturbation modeling, providing a valuable tool for accelerating therapeutic target discovery.

bioinformatics↗

bioRxiv2025

Structural semantic evolutionary distance (SSED) unifies the selection of cancer driver genes across macroevolution and tumorigenesis.

The non-random, site-specific enrichment of somatic mutations in cancer driver genes (CDGs) suggests their emergence is governed by underlying evolutionary constraints. However, quantitative methods to define these constraints and their underlying principles remain underexplored. To address this, we introduce the Structural Semantic Evolutionary Distance (SSED), a metric leveraging the pretrained ESM-3 protein language model to quantify evolutionary divergence within a unified structural semantic space. Our analysis demonstrates that CDGs are subject to persistent structural semantic constraints across species, tolerating a significantly narrower range of structural semantic changes during evolution compared to non-CDGs. Crucially, clinically observed oncogenic mutations follow this same principle, favoring minimal structural perturbation as shaped by long-term gene evolution. Such mutations maintain core protein function while conferring a capacity for immune evasion, thereby driving clonal expansion. Guided by this "evolutionary constraint" framework, we successfully predicted and experimentally validated a previously uncharacterized oncogenic mutation, KRAS R135L, in bronchial epithelial cells. Furthermore, clinical cohort analysis demonstrated that SSED acts as an independent predictor of response to immune checkpoint blockade, offering information orthogonal to tumor mutational burden (TMB). This study unifies the evolutionary principles governing CDGs across macroevolutionary and microevolutionary (tumorigenesis) timescales, elucidates the balance between structural adaptability, functional conservation, and immune pressure, and identifies a novel predictive biomarker for cancer immunotherapy.

genetics↗

bioRxiv2025

Comprehensive perturbation of transcription factors in human cardiomyocytes reveals the regulatory architecture of congenital heart disease

Transcription factors (TFs), including DNA binding proteins and epigenetic co-regulators, control the timing of gene programs during lineage commitment1. However, systematically defining the dynamic activities of the human genomes nearly 2000 TFs during development remains challenging2,3. Here, we use Perturb-Seq to map the transcriptional impact of nearly all human TFs and a subset of enhancers during cardiomyocyte differentiation. Our results suggest that developmental regulatory networks are distributed across highly connected hub TFs4-6 that are dynamic across lineage and time, rather than organizing into top-down hierarchies directed by "master regulators". We also identify distinct TF ensembles that regulate sequential decision points during cardiac cell-fate specification by coordinating lineage-specific activation with alternate lineage repression. Separately, analysis of TF-TF cooperativity uncovers a dynamic interaction between MEF2 family TFs7 and members of the Polycomb Repressive complex 18-10 to execute alternative fate repression. Building on these regulatory interactions, we construct a deep learning transformer model to accurately predict perturbed TFs driving altered regulatory networks in patient-derived transcriptomes. Together, our results define the regulatory network architecture of human lineage specification and provide a platform for predicting TF function and interpreting disease mechanisms.

genomics↗

bioRxiv2025

Retroreflective beam multiplexing enables high-throughput two-photon voltage imaging in vivo

Voltage imaging demands technical innovations to realize its full potential in neuroscience. Although two-photon microscopy is widely used in brain research, its imaging speed is insufficient for high-throughput voltage recordings. To overcome this limitation, we developed an all-optical beam multiplexing engine via retroreflection from two near-parallel mirrors. This approach integrates seamlessly with standard two-photon microscopes, enabling kilohertz-frame-rate imaging across a 16-fold expanded field of view while maintaining synaptic resolution. Operating at over 220 megapixels per second, it enables submillisecond imaging of dendritic propagation of action potentials and simultaneous voltage recording from more than 200 hippocampal neurons in head-fixed, behaving mice. This advancement unlocks new possibilities for large-scale, high-speed functional studies in neuroscience.

neuroscience↗

bioRxiv2025

Anatomical and molecular organization of the nociceptive medial thalamus

The medial thalamus (MTh) is a critical hub for integrating the affective and motivational dimensions of pain, yet its cellular and circuit organization remains poorly defined. Here, we combine activity-dependent genetic tagging, whole-brain clearing and light-sheet imaging, single-cell transcriptomics, and viral circuit tracing to build a comprehensive anatomical and molecular atlas of nociceptive and opioidergic neurons within the MTh. We show that acute and chronic pain activate distinct, spatially localized microdomains across multiple MTh subnuclei, including the central medial, interanteromedial, mediodorsal, and xiphoid nuclei. Activity-dependent tagging reveals a stable ensemble of nociceptive neurons that remains engaged across acute and chronic pain states, suggesting persistent thalamic encoding of affective nociception. Using fluorescent in situ hybridization, we find that most nociceptive-activated neurons express Oprm1, and that nearly all Oprm1+ neurons are activated by nociceptive stimuli, identifying a pain-active, {micro}-opioid receptor-expressing population in MTh (MThMOR). Rabies-based tracing demonstrates that MThMOR neurons receive convergent inputs from nociceptive and inhibitory regions including the anterior cingulate cortex, periaqueductal gray, parabrachial nucleus, and habenula, while projecting broadly to cortical, subcortical, and brainstem structures involved in pain, arousal, and motivation. Enkephalinergic inputs to MTh arise from distinct, non-nociceptive populations, suggesting parallel pathways for nociceptive transmission and endogenous opioid modulation. Together, these findings define the anatomical and molecular organization of the nociceptive medial thalamus and highlight MThMOR neurons as a cell-type-specific substrate for the development of targeted opioid-based pain therapies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=57 SRC="FIGDIR/small/692629v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@a1e6b3org.highwire.dtl.DTLVardef@13112eborg.highwire.dtl.DTLVardef@d125caorg.highwire.dtl.DTLVardef@107fd80_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

AAV vectors with enhancer-controlled ITR promoters

Adeno-associated virus (AAV) is limited by its packaging capacity and the unwanted promoter activity of inverted terminal repeats (ITRs). Here we utilized mini-enhancers to regulate ITR promoters and drive AAV cargo expression in the absence of the canonical promoters, which not only solved the ITR issue but also released more payload for the cargo. As an example, this new design successfully enabled robust, tissue-specific SpCas9 gene editing via a single AAV, which otherwise requires a dual-AAV system due to the large size of SpCas9.

bioengineering↗

bioRxiv2025

Rapid robust high-fidelity 3D neuronal extraction from multi-view projections

Recent developments in imaging facilitate large-scale three-dimensional (3D) neuronal recording. While these huge amounts of data shed new light on population-level neural coding, it is much harder to extract neuronal calcium dynamics from 3D volumes than 2D images with the existence of noise and scattering. Here, we presented DeepWonder3D, a general end-to- end pipeline for rapid and robust 3D neuronal extraction with high fidelity. Instead of processing voxel by voxel, DeepWonder3D works on the multi-view projections of 3D imaging data obtained either digitally or optically through specific point spread functions (PSFs) for general applicability to diverse techniques, including point-scanning microscopy, light- field microscopy, and two-photon synthetic aperture microscopy. Integrating denoising, resolution registration, background removal, neuronal extraction, and multi-view fusion into a unified pipeline tailored for large-scale high-resolution datasets contaminated by noise and scattering, DeepWonder3D outperforms state-of-the-art methods in 3D localization accuracy with a 10-fold reduction in computational costs, validated by numerical simulations and a hybrid two-photon/light-field imaging system. With the RUSH3D mesoscope, DeepWonder3D achieves rapid high-fidelity 3D calcium extraction of tens of thousands of neurons across the mouse cortex within hours.

neuroscience↗

bioRxiv2025

Adapting Epigenetic Clocks for Cell-Free DNA High-Throughput Sequencing Data

Background.Circulating cell-free DNA (cfDNA or ccfDNA) methylation sequencing holds promise for developing epigenetic aging clocks in minimally invasive aging assessment applications. However, current clocks--primarily trained on array-based data--do not readily generalize to methylation profiles of cfDNA, due to stochasticity and uncertainty arising from the limited input amounts of cfDNA and technical characteristics of high-throughput sequencing (HTS) platform. Due to lack of training to correct this uncertainty, direct application of legacy clocks to HTS data will inevitably produce unreliable estimates, introduce predictive discordance and undermine the trustworthiness of epigenetic biomarkers. Despite this urgent challenge, a systematic, model-agnostic framework for adapting existing epigenetic clocks to HTS-based cfDNA data remains lacking. Methods.Here, we generated a dedicated benchmark dataset comprising paired cfDNA and genomic DNA (gDNA), which was replicated and profiled across two methylation arrays and two targeted HTS platforms. We evaluated 53 epigenetic clocks for CpG coverage, reproducibility, cross-platform consistency, and age prediction accuracy. Further, we systematically explored and tested multiple adaptation strategies including depth filtering, beta-value imputation, and transfer learning via model distillation aiming at improving performance and clinical concordance of legacy epigenetic clocks on cfDNA HTS datasets. Results.Our results show that inherent technical noise of HTS platforms compromises diagnostic precision, presenting as a significant burden for applying legacy clocks on cfDNA HTS data. However, this technical limitation can be systematically neutralized. By enforcing stringent sequencing depth protocols ([≥]10x ideally 20x), employing robust algorithmic stabilization (L2-heavy clocks and imputation) and transfer learning, we can effectively isolate genuine physiological aging signals from technical artifacts. Ultimately, an adaptation pipeline incorporating all these methods effectively improved age prediction accuracy and, closed the gap between epigenetically induced aging status and clinically assessed realities. Besides, the pipeline demonstrated improved diagnostic sensitivity for neurodegenerative conditions such as amyotrophic lateral sclerosis, establishing a reliable foundation for non-invasive clinical monitoring. Conclusions.This study provided a comprehensive framework and practical guidelines for adapting epigenetic clocks to HTS-based cfDNA data, paved the path for more general application of cfDNA-based aging assessment and liquid biopsies.

bioinformatics↗

bioRxiv2025

RNA editing fine-tunes transcriptional plasticity and enhances the adaptability of Myzus persicae to diverse host plants

Parthenogenetic organisms can adapt to diverse and rapidly changing environments despite limited standing genetic variation, but the molecular mechanisms enabling such adaptability remain unclear. Here, we investigate this question in the green peach aphid (Myzus persicae, GPA), an asexual generalist herbivore capable of colonizing a wide range of host plants without underlying genetic change. By integrating RNA-seq and DNA-seq from genetically identical clones reared on different hosts, we identified 1,368 high-confidence RNA editing sites (RES), many of which exhibited strong host-dependent differences in editing levels. These RES encompassed all 12 possible nucleotide substitutions, with A-to-I, C-to-U, and U-to-C conversions being particularly prevalent. Editing at several sites shifted dynamically within 48 hours of host transfer and often coincided with changes in transcript abundance. Functional knockdown of the editing genes ADAR1 and ADAR2 reduced editing at specific sites, diminished fecundity, and abolished aphid survival on new hosts. Comparative analyses across aphid species reveal that although the biochemical signatures of A-to-I editing are deeply conserved, the genomic locations and functional roles of edited transcripts are species specific, reflecting lineage-specific adaptive strategies. Together, our findings demonstrate that RNA editing provides a rapid, reversible mechanism for environmental acclimation in GPA, enabling adaptive phenotypic plasticity even in the absence of genetic variation. This work establishes RNA editing as a key molecular basis for the remarkable ecological generalism of clonal organisms. Significance statementA major question in evolutionary biology is how clonal organisms with little genetic variation rapidly adapt to diverse, changing environments. Here we show that RNA editing provides a mechanism enabling the parthenogenetic green peach aphid (Myzus persicae) to colonize a wide range of host plants. RNA editing generates transcriptomic diversity, responds quickly to host shifts, and is essential for adaptation, as silencing ADAR genes disrupts A-to-I editing, reduces fitness, and prevents survival on new hosts. Comparative analyses across aphid species reveal that although the biochemical features of A-to-I editing are conserved, its genomic deployment and functional outcomes differ among species, reflecting lineage-specific strategies. These findings demonstrate that RNA editing creates a dynamic regulatory layer that offsets constraints of asexual reproduction.

molecular biology↗

bioRxiv2025

Alphaviral nonstructural protein-host RBP co-condensation as a mechanism to sustain virus replication

It has long been recognized that the intracellular replication of alphaviruses critically relies on several key host RBPs, including G3BP1/2 and FXR1/FXR2/FMR1, but how these RBPs modulate alphaviral replication and whether it would be possible to target these RBPs for antiviral treatment are less explored. Here, using SFV as a model, we report that SFV nsP3 exploits G3BP for its condensation and transforms antiviral stress granules into proviral nsP3-G3BP co-condensates. The gel-like co-condensates of nsP3 and G3BP enrich and protect viral genomic RNAs from host RNase degradation and serve as viral translational hubs to promote viral replication. The mode of nsP3-RBP co-condensation is prevalent across alphaviruses, and disruption of nsP3 condensates is an efficient antiviral approach. Thus, these findings uncover a general anti-alphavirus strategy based on the conserved reliance of nsP3-RBP co-condensation.

cell biology↗

bioRxiv2025

RNA degradation modulates unique aging-related gene expression in naked mole-rats

Gene expression is co-regulated by the rates of RNA synthesis and degradation, and recent evidence has linked their imbalance to the onset of aging. The naked mole-rat (NMR) is a small rodent with an exceptionally long lifespan and markedly delayed aging, yet little is known about its RNA synthesis and degradation characteristics compared to other rodents that age more rapidly. Here, we investigate RNA synthesis and degradation in NMR and mouse skin fibroblasts by monitoring incorporation of a uridine analog, 4-thiouridine. Cross-species analysis showed that the NMR cells have higher overall rates of RNA synthesis and degradation. It further revealed higher RNA degradation rates in aging-related pathways, notably Mtorc1 signaling, likely contributing to reducing the overall expression. Although known aging-associated genes, including Xrcc5, Nudt1, Fen1, and Aptx, were expressed at similar levels in NMR and mouse fibroblasts, the RNA turnover rates were largely altered. To uncover the underlying mechanism enabling differential control of RNA kinetics, we analyzed the transcript feature importance by machine learning and identified key features governing RNA degradation both common and unique in NMR and mouse fibroblasts. Our data highlight a potential role of RNA synthesis and degradation as hidden layers of gene regulation in NMR.

molecular biology↗

bioRxiv2025

MPKaDB: A pKa Database for Exploring pH Dependence in Membrane Proteins

The biological activities of many membrane proteins are pH-regulated, yet mapping their pH dependence experimentally is slow and expensive. In this work, we present MPKaDB (http://computbiophys.com/DeepKa/mpkadb), a comprehensive pKa database for membrane proteins that instantly decode the protonation states of ionizable residues under a specified pH. Leveraging MPKaDB, we performed pH-coupled electrostatic characterization of trans-membrane proteins. To facilitate use, a user-friendly search engine was developed to retrieve a protein of interest and returns its pKa values, isoelectric points of both cytoplasmic and extra-cytoplasmic faces, and an automated screening of active-site residues. In the end, two case studies were proposed to demonstrate how pKas from MPKaDB could be applied to explore the pH-dependent relationship between membrane protein structure and function. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/688495v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@f90726org.highwire.dtl.DTLVardef@1448ac2org.highwire.dtl.DTLVardef@f1e4f4org.highwire.dtl.DTLVardef@ee57dc_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Recurrent Breast Cancer Cells Depend on De novo Pyrimidine Biosynthesis to Suppress Ferroptosis

Breast cancer recurrence remains a major clinical challenge, often associated with therapy resistance and altered metabolic states. To define metabolic vulnerabilities of recurrent disease, we performed a CRISPR knockout screen targeting 421 metabolic genes in paired primary and recurrent HER2-driven breast cancer cell lines. While both primary and recurrent tumors shared dependencies on core metabolic pathways, recurrent tumors exhibited selective essentiality for the de novo pyrimidine synthesis pathway, including Cad, Dhodh, and Ctps. Pharmacologic inhibition of the rate-limiting enzyme DHODH with BAY-2402234 selectively impaired the growth of recurrent tumor cells, while primary tumor cells were relatively resistant. BAY treatment robustly inhibited pyrimidine synthesis in all lines, but only recurrent cells underwent iron-dependent lipid peroxidation and ferroptotic cell death. Lipidomic profiling revealed enrichment of polyunsaturated ether phospholipids in recurrent cells, which may predispose them to ferroptosis. A sensitizer CRISPR screen in primary cells further identified nucleotide salvage and lipid metabolic pathways as modifiers of DHODH inhibitor sensitivity. Stable isotope tracing and nutrient depletion experiments showed that primary cells can compensate for DHODH inhibition through nucleotide salvage, whereas recurrent cells exhibit impaired salvage capacity, likely due to reduced expression of Slc28/Slc29 nucleoside transporters. Together, these findings reveal that breast cancer recurrence is associated with increased dependence on de novo pyrimidine synthesis to suppress ferroptosis, highlighting a therapeutically actionable metabolic vulnerability in recurrent disease.

cancer biology↗

bioRxiv2025

SpaTranslator: A deep generative framework for universal spatial multi-omics cross-modality translation

Recent advances in spatial omics technologies have enabled the simultaneous analysis of multiple molecular patterns in tissue sections, offering unprecedented insights into cellular microenvironments. However, the high cost of measurements and the sparsity of data restrict the availability of paired spatial multi-omics datasets. Here, we present SpaTranslator, a deep generative framework that integrates graph neural networks with an adversarial variational generative model to fully capture spatial characteristics and enable effective cross-modality translation of spatial omics data, enabling simulation of paired spatial multi-omics data from single-omics measurements. Extensive experiments demonstrate that SpaTranslator consistently outperforms baseline methods in both clustering accuracy and biological coherence across various real-world scenarios, including spatial transcriptomics-epigenomics and spatial transcriptomics-proteomics translation tasks. Furthermore, SpaTranslator provides biologically meaningful insights through marker genes and proteins recovery, motif enrichment analysis, and gene regulation inference. Our work offers an effective and adaptable solution for spatial multi-omics cross-modality translation, supporting a broad range of biological and biomedical research.

bioinformatics↗

bioRxiv2025

YAP1 Depletion Enhances TAZ and its Complexation with TEAD4 and AP-1 Heterodimer C-JUN/FOSB to Promote Gastric Cancer Progression and Metastases

BackgroundDysregulation of the Hippo signaling pathway, characterized by aberrant activation of the transcriptional coactivators YAP1 and TAZ, drives tumour progression, immunosuppression and metastasis. Hippo pathway components are emerging therapeutic targets in several solid tumours, however, the expression profiles of Hippo coactivators YAP1, TAZ and their transcriptional factors TEAD1-4 in gastric cancer peritoneal metastases (GCPMs) and their therapeutic value are unknown. ObjectiveTo determine expression status of YAP1, TAZ and TEAD1-4 in GCPMs; and to evaluate whether dual targeting of YAP1 and TAZ provides superior antitumour activity compared with inhibition of either coactivator alone. DesignExpression of YAP1, TAZ and TEAD1-4 was examined in GCPMs by single-cell RNA sequencing and co-immunofluorescent staining. Functional studies using genetic knockout and antisense oligonucleotide (ASO) inhibition of YAP1 or TAZ were performed to assess antineoplastic effects in vitro and in vivo. Co-immunoprecipitation and luciferase reporter assays were used to characterize YAP1/TAZ interactions with TEADs and AP-1 components (JUN and FOSB) and to quantify transcriptional activity. Antitumour efficacy was validated in patient-derived xenograft (PDX) and KP-Luc2 syngeneic models. ResultsYAP1, TAZ, and TEADs1- 4 were highly coexpressed in GCPMs and correlated with poor survival. YAP1 inhibition alone elicited compensatory upregulation of TAZ, while combined inhibition of both coactivators maximally repressed cell proliferation and invasion in vitro, and tumor growth in vivo. Increased TAZ complexation with TEAD4 and AP-1 (c-JUN and FOSB) heterodimer was observed following YAP1 knockdown or pharmacological ASO inhibition. Dual inhibition of YAP1 and TAZ was required to maximally suppress YAP1/TAZ expression and reduce their nuclear accumulation, transactivation of TEAD, and activation of downstream genes. ConclusionsThese findings show that combined YAP1 and TAZ inhibition holds promise for the treatment of GCPMs, a highly lethal disease with an urgent need for novel treatment options. WHAT IS ALREADY KNOWN ON THIS TOPICO_LIGastric cancer with peritoneal metastasis (GCPM), occurring in > 45% of gastric cancer (GC) patients, is a highly lethal malignancy with limited therapeutic options. C_LIO_LIThe Hippo pathway mediator Yes-associated protein 1 (YAP1) is intimately involved in chemoresistance, cancer stemness properties, and the epithelial-to-mesenchymal transition in gastric and other cancers. C_LIO_LIWhile YAP1 represents a promising therapeutic target, clinical trial of YAP1 antisense oligonucleotides has been disappointing. C_LI WHAT THIS STUDY ADDSO_LIHippo coactivators YAP1, TAZ and their main transcription factors TEAD1-4 are markedly upregulated in GCPMs and associated with poor prognosis. C_LIO_LIAntisense targeting of YAP1 results in compensatory upregulation of its paralog TAZ. C_LIO_LIUpon YAP1 depletion, TAZ forms transcriptional complexes with TEAD4 and the AP-1 heterodimer (JUN and FOSB). C_LIO_LIDual targeting of YAP1 and TAZ, by oligonucleotides, achieves maximal suppression of tumour growth in vitro and in vivo. C_LI HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYO_LIThese findings provide a strong mechanistic rationale for co-targeting YAP1 and TAZ as a therapeutic approach in metastatic gastric cancer. C_LIO_LIDual Hippo coactivator inhibition could inform the design of future clinical trials aimed at improving outcomes for patients with GCPMs. C_LI

cancer biology↗

bioRxiv2025

Tuning a Genetic Circuit with Double Negative Feedforward Loops to Approximate Square Waves

Precise temporal control of gene expression is important for programming cellular functions. Existing circuits, however, often couple amplitude and duration. This prevents independent tuning of key dynamic features. We therefore set out to design a genetic system capable of generating square-wave outputs with externally programmable geometry. To achieve this, we constructed a layered regulatory design that separates production and removal into two independently controlled modules. An activating input turns expression on and builds the reporter. A repressing input stops synthesis and removes existing protein. Together, these actions confine the active window and produce square-wave outputs or pulses on demand. Waveform geometry depends on input dose and timing. Analysis of limiting cases reveals that strong repression compresses dynamic range, and finite degradation capacity restricts decay rate. Enhancing removal capacity alleviates this bottleneck and sharpens the off-transition. Together, this work establishes a general framework for programming gene-expression dynamics with independently tunable amplitude and duration.

synthetic biology↗

bioRxiv2025

Compositional analysis of yellow fever virus induced stress granules reveals a functional connection to mitochondrial homeostasis

The phase separation of biomolecules into so-called stress granules (SGs) allows the cell to tightly regulate translation activity in response to different stimuli, such as oxidative stress, starvation, or the recognition of non-cellular RNA. Recent reports suggest SGs induced during viral infection, may act as a crossroad between the cellular stress response and the activation of the innate immune response. Here, we aimed to dissect the role of SGs in the context of yellow fever virus (YFV) infection. We found that YFV infection resulted in translational shut-off from 24 hpi on followed by the formation of SGs at 48 hpi, a delay potentially associated with the ability of the YFV capsid to inhibit SG formation, through an interaction with the major SG scaffolding protein G3BP1. To elucidate the role of YFV-induced SGs during infection, we inhibited SG assembly using a small-molecule inhibitor and find that SG formation does not influence viral replication. Uncovering the first proteome of virus-induced SGs, our compositional analysis revealed a specific enrichment of proteins associated with mitochondrial processes in YFV-induced SGs. Indeed, we show that YFV infection results in mitochondrial damage and dysfunction. Together, we propose that YFV-induced SGs may be involved not only in the modulation of cellular homeostasis but also in influencing mitochondrial functions. Author SummaryViruses impose a major burden on the infected host - from structural rearrangements needed to assemble replication complexes, to exploiting cellular energy resources and genetic rewiring associated with antiviral responses. The assembly of membrane-less organelles such as stress granules (SGs) enable cells to rapidly tune cellular processes upon sensing of stresses such as viruses. Moreover, the cells innate immune response is proposed to be regulated by SGs and in turn many viruses disrupt or highjack their components. Yet, the molecular basis for SG functions during infection remain ambiguous. Here we investigated the interplay between yellow fever virus (YFV) infection and SGs. We demonstrate that infection with attenuated or pathogenic viruses result in the formation of SGs. Their compositional analysis reveal that they sequester mitochondrial proteins, correlating with altered mitochondrial functions during infection. This highlights a novel complex interplay between membrane-bound and membrane-less organelles which could present novel opportunities for antiviral therapies.

microbiology↗