Biology subjects

Kim, K.

Publications and source records attributed to Kim, K..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Toward Single-Cell Control: Noise-Robust Perfect Adaptation in Biomolecular Systems

Robust perfect adaptation (RPA), whereby a consistent output level is maintained even after a disturbance, is a highly desired feature in biological systems. This property can be achieved at the population average level by combining the well-known antithetic integral feedback (AIF) loop into the target network. However, the AIF controller amplifies the noise of the output level, disrupting the single-cell level regulation of the system output and compromising the conceptual goal of stable output level control. To address this, we introduce a new regulation motif, the noise controller, which is inspired by the AIF loop but differs by sensing the output levels through the dimerization of output species. Combining this noise controller with the AIF controller successfully maintained system output noise as well as mean at their original level, even after the perturbation, thereby achieving noise RPA. Furthermore, our noise controller could reduce the output noise to a desired target value, achieving a Fano factor as small as 1, the commonly recognized lower bound of intrinsic noise in biological systems. Notably, our controller remains effective as long as the combined system is ergodic, making it applicable to a broad range of networks. We demonstrate its utility by combining the noise controller with the DNA repair system of Escherichia coli, which reduced the proportion of cells failing to initiate the DNA damage response. These findings enhance the precision of existing biological controllers, marking a key step toward achieving single-cell level regulation.

systems biology↗

bioRxiv2025

Parallelized Brightfield and Fluorescence Imaging of Organoids Using a Scalable Multi-Camera Platform

Organoid viability, maturation, and growth is commonly assayed through brightfield and fluorescence microscopy using a single objective lens. However, standard microscopic imaging systems pose significant limitations for high-throughput applications, particularly in large-scale experiments where simultaneous imaging of multiple organoids requires increased throughput. There is a strong need for systems that can capture organoid growth rapidly and consistently while minimizing disturbances to culture conditions. Here, we present a novel multi-camera array scanner (MCAS) that parallelizes imaging through the simultaneous use of 48 objective lenses and sensors, resulting in a 95% reduction in acquisition times compared to commercial high-content imagers. We demonstrate and validate this system in multiple well plate formats, in both 2D and 3D neural cell cultures, and in brightfield and fluorescence. The MCAS improves efficiency for measuring organoid growth rates, assessing responses to morphogens and drugs, and measuring viral transduction efficiency. Together, these findings establish the MCAS as a scalable and versatile imaging platform for rapid phenotyping in organoid research.

neuroscience↗

bioRxiv2025

Rapid discovery of antiviral targets through dimensionality reduction of genome-scale metabolic models

The COVID-19 pandemic underscored the urgent need for rapid and broadly applicable strategies to identify antiviral targets against emerging pathogens. Conventional approaches, which rely on detailed viral characterization and large-scale drug screening, are too slow to address this challenge. Here, we introduce a transcriptome-based computational framework that integrates genome-scale metabolic models with dimensionality reduction to uncover host metabolic vulnerabilities that support viral replication. Applying this approach to bulk and single-cell RNA-seq data from HCoV-OC43-infected cells and organoids identified oxidative phosphorylation as a key vulnerability, and pharmacological inhibition of complex I effectively curtailed viral replication. Extending the framework to SARS-CoV-2 and MERS-CoV revealed pyrimidine catabolism as a conserved antiviral pathway, with inhibition of its rate-limiting enzyme DPYD suppressing replication in organoid models. Re-analysis of SARS-CoV-2 patient metabolome data further confirmed elevated DPYD activity, underscoring its clinical relevance. Together, these findings establish a generalizable and rapid strategy for host-directed antiviral discovery, providing a foundation for precision therapeutics and pandemic preparedness. Significance StatementHost-directed antiviral therapies offer several advantages in antiviral research, but identifying key host factors poses a significant challenge. By integrating genome-scale metabolic models with single-gene knockout simulation and dimensionality reduction, we developed a computational framework based on single and bulk RNA-seq data that can systematically pinpoint host pathways whose downregulation is predicted to rewire virus-induced metabolic alterations. Applying this approach to multiple human coronaviruses reveals unique metabolic vulnerabilities, and we experimentally demonstrate that inhibiting these host metabolic pathways reduces viral replication. This framework provides a generalizable antiviral strategy to discern effective targets and can be further extended to investigate virus-host metabolic interactions.

systems biology↗

bioRxiv2025

PSP-0119: Targeted IRAK4 Degradation as a Novel Therapeutic Strategy for FLT3-Mutant AML

Acute Myeloid Leukemia (AML) is a life-threatening hematologic malignancy. Despite recent therapeutic advances, rising incidence rates emphasize the urgent need for identification of new targets and therapies. Roles of interleukin receptor-associated kinases IRAK1/4 are emerging in hematologic and solid malignancies. In AML, IRAK4 mRNA is overexpressed at diagnosis, relapses, in residual disease, and in FLT3-ITD-mutant cells, MDS, MPN, and MDS/MPN-negative subtypes. Compared with hematopoietic stem cells, IRAK4 is elevated in t(15;17), inv(16)/t(16;16), and t(11q23)/MLL subtypes, correlating with poor survival. Here, we disclose anti-AML activity of PSP-0119, a novel IRAK4 PROTAC degrader. PSP-0119, inhibited IRAK4 kinase activity, NF-{kappa}{beta} activity, and IL-1{beta}-induced IRAK4 phosphorylation. In-silico docking revealed interactions in CRBN/IRAK4/PSP-0119 ternary complex. PSP-0119 degraded IRAK4 in FLT3-mutant AML cell lines sparing FLT3-wild-type AML cells, FLT3-wild-type patient samples, and normal bone-marrow. Bulk-seq of PSP-0119 treated MOLM-13 cells revealed downregulation of eNOS, a poor AML prognosticator. PSP-0119 suppressed colony formation, cell viability, and MOLM-13 xenograft growth, and synergized with IRAK1 covalent inhibitor JH-X-119-01. PSP-0119 is metabolically stable, retaining 71% of parent compound at 60 minutes in human liver microsomes. In summary, IRAK4 degradation via PSP-0119 as a promising therapeutic strategy for treatment of FLT3-mutant AML.

cancer biology↗

bioRxiv2025

Harnessing the Embryo Antitumor Factor NEPN for Broad-Spectrum Cancer Immunotherapy via Dual Modulation of Tumor Progression and Immune Suppression

Modifying the tumor microenvironment to target malignant cells and spare healthy cells may be an alternative approach to cancer therapy. Early-stage embryos have been shown to reprogram metastatic tumor cells and prevent tumor formation of several types of cancers, including melanoma, leukemia, and neuroblastoma. However, embryonic factors that suppress tumors in early embryos have not been identified. Here we show that the embryonic secretory factor NEPN suppresses cancer progression and enhances tumor-infiltrating T cells by modulating HSP27 and ARG1 through TGF{beta}1 signaling, together with broader regulation of tumor-promoting and immune-modulating cytokines. Importantly, NEPN strengthens immune responses and cell death in not only non-solid tumor but also solid tumors by increasing T cell infiltration and activity in the tumor microenvironment. The ability of NEPN to boost immune responses within the tumor microenvironment establishes it as a promising therapeutic candidate for cancer immunotherapy.

cancer biology↗

bioRxiv2025

High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles

Despite recent advances in data acquisition and algorithmic development, applying single particle cryogenic electron microscopy (cryoEM) to small proteins (<50kDa) remains challenging, even when high quality data are available, in part due to the lack of reliable low-resolution structural features to inform initial alignments. Here we present a workflow which effectively bypasses this step, by obtaining initial particle orientations directly from heterogeneous ab initio reconstruction in CryoSPARC solely using data at high spatial frequencies. Applying this approach, we solve the structure of a previously intractable protein in a publicly available dataset, iPKAc (EMPIAR-10252), 39 kDa, resolved at an estimated resolution of 2.7 [A] as well as a hemoglobin alpha-beta dimer (EMPIAR-10250) at 29kDa, resolved to an estimated resolution of 4 [A]. We also show that the Aca2-RNA complex (37kDa, EMPIAR-11918) can be resolved by this approach directly from a blob-picked particle stack, in a single round of heterogeneous ab initio reconstruction followed by local refinement. The map of iPKAc is of sufficient quality to autobuild 325 of 356 residues present in the original crystal structure using Modelangelo, and ordered ATP and magnesium ions can clearly be resolved. The Hb-dimer has clear secondary structural features, identifiable hemes, and visible bulky sidechains, consistent with the estimated resolution. We expect that this approach may be useful for cryo-EM analysis of other small particles near or below the theoretical size limit.

biophysics↗

bioRxiv2025

Biomarker Discovery via Integrative Multi-omics for Children exposed to Humidifier Disinfectant

RationaleExposure to humidifier disinfectants has been linked to an array of pulmonary disorders and diminished lung functionality particularly reduced Forced Vital Capacity (FVC). ObjectivesThis investigation sought to identify diagnostic biomarkers for early detection of children at elevated risk of developing chronic respiratory conditions following such exposure. MethodsOur research employed a comprehensive multi-omics strategy analyzing 70 pediatric patients alongside 10 controls, seamlessly integrating clinical assessments with transcriptomics, methylomics, proteomics, and metabolomics data. The analytical framework utilized a sophisticated combination of Non-negative Matrix Factorization (NMF), Multi-Omics Factor Analysis (MOFA), and advanced machine learning algorithms. Measurements and Main ResultsNMF clustering uncovered distinctive protein expression patterns associated with integrin-mediated signaling pathways and immune response mechanisms. Complementarily, MOFA identified latent factors correlating with lung function metrics, highlighting critical molecular pathways involved in integrin cell surface interactions and lipid metabolism regulation. Machine learning-based analysis facilitated the development of a multi-marker panel-comprising IGHV2-70, LysoPC (16:0), and hexadecyl ferulate-which achieved 81.46% accuracy in identifying pulmonary dysfunction cohort. ConclusionsThese findings suggest that alterations in integrin-related signaling networks and dysregulation of lipid metabolism play pivotal roles in mediating the long-term pulmonary consequences of humidifier disinfectant exposure. The proposed multi-marker panel offers significant potential for enhanced risk stratification and timely therapeutic intervention. At a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSExtensive epidemiological evidence has established the causal relationship between humidifier disinfectant exposure and pulmonary dysfunction; however, clinically validated biomarkers for predicting chronic lung disease progression remain limited. Pediatric populations demonstrate unique pathophysiological mechanisms distinct from adults, highlighting the critical necessity for biomarker identification grounded in comprehensive molecular understanding. Despite advances in omics technologies, recent investigations have encountered significant obstacles in achieving deeper mechanistic insights, predominantly attributable to methodological constraints in harmonizing clinical phenotypes with high-dimensional molecular datasets. What This Study Adds to the FieldThis investigation elucidates the fundamental contributions of integrin-mediated signaling cascades and lipid metabolic networks to persistent pulmonary dysfunction following humidifier disinfectant exposure. Our analyses revealed coordinated regulation of integrin signaling pathways and immune response networks through NMF clustering, indicating dynamic temporal evolution of inflammatory responses during chronic disease progression, with temporally distinct molecular signatures identified across discrete observation intervals. Multi-omics factor analysis (MOFA) corroborated integrin pathway dysregulation while additionally uncovering systematic suppression of lipid metabolic processes. Furthermore, machine learning algorithms enabled development of a robust three-component biomarker panel--encompassing IGHV2-70, LysoPC (16:0), and hexadecyl ferulate--demonstrating 81.46% classification accuracy for pulmonary dysfunction phenotypes. Collectively, these findings substantially advance mechanistic understanding of chronic lung injury in vulnerable pediatric cohorts and identify clinically relevant biomarkers with translational potential for risk stratification and therapeutic targeting in clinical practice.

systems biology↗

bioRxiv2025

Interferon gamma signaling drives cardiac metabolic rewiring

BackgroundIFN-gamma (IFN-{gamma}) signaling influences myocardial inflammation and fibrosis across a wide range of conditions, including ischemic and non-ischemic heart failure (HF). However, the direct effects of IFN-{gamma} on cardiomyocytes remain poorly understood. Here, we developed a novel in vivo model to investigate how IFN-{gamma} impacts myocardial metabolism and function. MethodsMale C57BL/6J mice were injected intravenously with hepatotropic adeno-associated virus (AAV2/8) carrying Ifng and nLuc reporter under the albumin promoter (AAV- Ifng) or empty vector control virus (AAV-ctrl). Cardiac alterations were monitored on day 28 through flow cytometry, bulk RNA sequencing, targeted metabolomics, isolated mitochondrial activity, echocardiography, and in vivo imaging using [18F]fluordeoxyglucose ([18F]FDG) and [18F]fluoro-6-thia-heptadecanoic acid. Additionally, mice lacking IFN-{gamma} receptor expression in cardiomyocytes (Myh6Cre Ifngr1fl/fl) were used to further dissect the cell-intrinsic roles of IFN-{gamma} signaling in cardiomyocyte metabolic reprograming. ResultsAfter confirming liver-specific viral transfection and elevated serum IFN-{gamma} production at physiological levels, we observed cardiac metabolic adaptation and rewiring in animals treated with AAV-Ifng compared to control animals. Myocardial bulk RNA sequencing and gene set enrichment analysis identified an IFN-{gamma} response signature accompanied by marked down-regulations of oxidative phosphorylation and fatty acid oxidation pathways. Functional assessment of isolated cardiac mitochondria showed decreased oxygen consumption, and targeted metabolomics confirmed metabolic shifts toward glycolysis in mice overexpressing IFN-{gamma}. In vivo imaging confirmed increased cardiac glucose uptake following AAV-Ifng treatment. Notably, these metabolic alterations were abrogated in mice with cardiomyocyte-specific deletion of IFN-{gamma} receptors (IFNGR). ConclusionsSystemic IFN-{gamma} induces pronounced metabolic reprogramming in the heart, characterized by increased glucose uptake and reduced oxidative phosphorylation, via direct signaling through cardiomyocyte IFNGR. These alterations mirror those observed in aging and some forms of HF, thereby highlighting that, beyond classical inflammation, this cytokine regulates cardiac metabolism. Novelty and significanceO_ST_ABSWhat is known?C_ST_ABSO_LIImmunological mechanisms can impact myocardial disease progression through complex context-dependent mechanisms. C_LIO_LIIFN-{gamma}, a cytokine primarily secreted by natural killer and T cells, promotes myocardial inflammation and fibrosis in the context of autoimmune myocarditis, pressure-overload-induced heart failure, and Chagas cardiomyopathy. C_LIO_LICytokines exert pleiotropic effects and can influence inflammatory responses through mechanisms involving control of energy metabolism. C_LI What new information does this article contribute?O_LIA novel adeno-associated virus model of systemic IFN-{gamma} elevation allows assessment of cardio-immune-metabolic crosstalk without confounding factors. C_LIO_LIIFN-{gamma} drives cardiac metabolic reprogramming in inflammatory contexts, characterized by enhanced glucose uptake and glycolysis with mitochondrial dysfunction, ultimately altering cardiac metabolic fluxes and function. C_LIO_LIThe IFN-{gamma}-induced cardiac metabolic reprogramming is, at least in part, mediated through direct signaling via receptors on cardiomyocytes. C_LI

immunology↗

bioRxiv2025

Hepatocyte FAM210A deficiency disrupts mitochondrial function and triggers juvenile steatosis with compensatory repair in adulthood

Mitochondrial dynamics are central to maintaining liver metabolic homeostasis, yet the mechanisms that safeguarding mitochondrial integrity during development and metabolic dysfunction remain poorly defined. Here, we identify Family with sequence similarity 210 member A (FAM210A) as a hepatocyte-enriched mitochondrial regulator essential for postnatal liver maturation. Hepatocyte-specific deletion of Fam210a (Fam210aHKO) in mice caused early growth restriction, reduced body and liver mass, and pronounced hepatic steatosis with glycogen depletion. These defects were accompanied by lower postprandial glucose levels in the fasted-refeeding state, impaired oxidative phosphorylation, reduced mtDNA content, and abnormal cristae architecture. Transcriptomic and proteomic profiling revealed broad suppression of fatty acid, sterol, and bile acid metabolism, with concomitant glutathione stress responses. Mechanistically, FAM210A deficiency disrupted the YME1L-OPA1 axis, driving excessive OPA1 cleavage and cristae destabilization. Strikingly, these juvenile defects were transient and resolved by adulthood, underpinned by enhanced hepatocyte proliferation and mitochondrial biogenesis, consistent with a compensatory stress-adaptive response via the activation of ISR signaling. Together, these findings uncover FAM210A as a developmental safeguard of mitochondrial remodeling in hepatocytes and indicate compensatory programs with therapeutic relevance for chronic liver disease.

physiology↗

bioRxiv2025

GCN5-TADA2B in the SAGA complex provide constitutive fine-tuning control of XRCC1 recruitment and focal retention at DNA damage sites.

The scaffolding protein XRCC1 orchestrates base excision repair (BER) and DNA single strand break repair (SSBR) through extensive protein-protein interactions, and its disruption contributes to human neurological diseases such as SCAR26. Recruitment to DNA damage sites has been traditionally understood to depend exclusively on interaction with PARP1 and PARP1 mediated PARylation. Here, we report for the first time the discovery of GCN5 and TADA2B, components of histone acetyltransferase module of SAGA complex, as novel XRCC1 binding partners that provide critical fine-tuning control over repair site localization. We demonstrate that these SAGA complex components bind XRCC1 constitutively via distinct BRCT domain interactions -- GCN5 mainly to BRCT I and TADA2B mainly to BRCT II -- independent of DNA damage status or GCN5s acetyltransferase activity. Depletion of either protein significantly impairs XRCC1 recruitment efficiency, while paradoxically rescuing focal retention defects in BRCT II deficient XRCC1 mutants. This dual regulatory behavior reveals a regulatory mechanism where constitutive protein interactions optimize normal XRCC1 function but become counterproductive when XRCC1 is structurally compromised, particularly in the BRCT II domain. Analysis of the SCAR26 associated variant, which disrupts TADA2B binding while maintaining LIG3 interaction, confirms this dual regulatory model and provides molecular insights into potential disease pathophysiology. Our findings establish a ready-for-action model of DNA repair coordination where protein complexes pre-organize repair machinery for immediate deployment upon damage detection, expanding our understanding of BER regulation.

cell biology↗

bioRxiv2025

Loss of brain insulin production impairs learning and memory in female mice

Diabetes is characterized by dysfunctional insulin release and action, and it is a risk factor for Alzheimers disease, the most common form of dementia. Alterations in brain insulin signalling and metabolism have been linked with Alzheimers disease. The ancestral insulin gene, Ins2, is transcribed locally within the brain. Here we demonstrate that hippocampal Ins2 mRNA is higher in females than males, and modulated by diet. To specifically determine how locally-produced insulin influences hippocampal function, we used mice with germline Ins2 knockout (Ins2-/-) and the normal complement of wildtype Ins1 alleles. Compensation from the Ins1 gene ensured normal glucose tolerance, normal insulin sensitivity, normal fasting insulin, and normal body weight under these conditions. Using the Morris water maze, we found that visuo-spatial learning and memory performance of female Ins2-/- mice was significantly impaired relative to wild-type mice, whereas the performance of male Ins2-/- and wild-type mice did not differ. We profiled isolated hippocampi from female Ins2-/- and littermate control mice using RNA sequencing to provide an unbiased analysis of gene expression differences that underlie these behavioural changes. Cyclin D1 (Ccnd1) was significantly reduced in Ins2-/- mice, prompting us to examine adult neurogenesis using exogenous mitotic marker EdU and the immature neuronal marker doublecortin (DCX). Our data demonstrate female-specific roles for brain-derived Ins2 on learning and memory function in mice. Research in contextO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIAlzheimers disease and type 2 diabetes share common risk factors and metabolic dysfunction. C_LIO_LIInsulin and insulin signalling are known to have positive effects on neuronal health and cognition. C_LIO_LILocal insulin production has been reported in the brain, including the hippocampus, which plays critical roles in learning and memory, as well as Alzheimers pathophysiology. C_LI What is the key question?O_LIWhat are the consequences of deleting the Ins2 gene, which selectively prevents local brain insulin production, on learning and memory in mice? C_LI What are the new findings?O_LIHippocampal insulin production via the Ins2 gene is sexually dimorphic and modulated by diet. C_LIO_LIKnocking out brain insulin production in Ins2-/- mice does not have significant effects on glucose homeostasis in these diet and housing conditions. C_LIO_LIKnocking out brain insulin production in Ins2-/- mice results in learning and memory impairments in female but not male mice. C_LI How might this impact on clinical practice in the foreseeable future?O_LIThese pre-clinical observations demonstrate a causal role for insulin in learning and memory, but will require additional human studies before they can impact clinical practice. C_LI

physiology↗

bioRxiv2025

Fine-tuning cell-mimicking polyacrylamide microgels: Sensitivity to microscale reaction conditions in droplet microfluidics

The ability to shape polyacrylamide (PAAm) hydrogels using droplet microfluidics enables the production of microgel particles that mimic the cellular physical properties, opening new avenues in mechanobiology. Precisely controlling microgel size and elasticity is crucial yet complex, as various factors influence polymerization and the resulting network structure. While it is well established that chemical reactions in microdroplets are typically faster and more homogeneous than in bulk systems, an often-overlooked aspect is the increased sensitivity of these microreactors: minor variations in chemical or physical parameters can lead to significant changes in the resulting microgel properties. Our study identifies flow conditions as a key factor influencing both microgel elasticity and size, by modulating interfacial transport during gelation. Using a flow-focusing microfluidic chip, we generated pre-gel droplets with identical composition dispersed in an oil phase, systematically varying the PAAm-to-oil flow rate ratio while keeping the total flow rate constant. This approach yields droplets with minimal diameter variation (<1 {micro}m), yet produces beads with distinct Youngs moduli, despite identical total monomer concentrations. Further analysis revealed that the catalyst transport across the oil-water interface significantly affects the polymerization efficiency and polymer network. Our findings highlight that despite the advantages of droplet-based polymerization, achieving reproducible microgel properties requires careful control of flow parameters. This underscores the importance of precise microfluidic control in advancing PAAm microgel applications in biophysics.

biophysics↗

bioRxiv2025

Divergence of an extracellular contractile injection system infectivity elucidated by high resolution structural studies of its tail-baseplate complex

Divergence to the infectivity practice by extracellular contractile injection systems (eCISs) is displayed by myophage P1 in its lytic phase involving its baseplate receding away from the host bacterium during infection. Atomic structure of the proteins forming P1s Tail Baseplate (TB) complex, determined here, using cryo electron microscopy are employed to identify a sequence of viral events explaining this unique phenomenon. The P1 baseplate is found to be devoid of protein appendages that are necessary for anchoring it to the host bacterium. To compensate this deficiency, P1s Long Tail Fibers (LTFs) affix to the hosts exterior, straighten up imparting stability to the virion for pursuing the infection process, thereby eliciting the baseplate hub and the tail sheath to ascend away, resulting in uniform compression of the latter. Upon the maximum unkinking of LTFs, a descending corkscrew motion commences that results in the non-uniform downward compression of the tail sheath, the tail tube and baseplate needle that perforates through the hosts membrane-cytoplasm, leading to a successful phage-bacterium infection.

biophysics↗

bioRxiv2025

High-throughput multi-camera array microscope platform for automated 3D behavioral analysis of freely swimming zebrafish larvae

Understanding the behavioral and morphological dynamics of moving model organisms like the zebrafish larvae requires accurate, high-throughput 3D analysis. However, traditional single-view 2D video tracking fails to capture the full scope of natural 3D movements and postural dynamics. Here, we present a novel high-throughput 24-camera array microscope with a co-designed "mirrored well plate" that allows for snapshot imaging of up to 48 wells over a 118 mm x 82 mm field of view from two orthogonal directions (i.e., a top-view and side-view). Accurate 3D position estimation and tracking is achieved with an efficient machine learning algorithm that scales well to high-throughput measurements. The proposed approach automates parallelized 3D model organism behavioral analysis, providing 3D skeletal tracking, swim bladder morphological dynamics, and kinematics of up to 48 swimming zebrafish larvae at up to several hundred frames per second. The result is an efficient and scalable solution for high-throughput 3D behavioral studies with broad compatibility with standard workflows across laboratories and procedures working with pharmacology, toxicology, and neuroscience.

animal behavior and cognition↗

bioRxiv2025

Transient YAP/TAZ inhibition exposes therapeutic vulnerabilities in advanced cancers

YAP and TAZ, key effectors of the Hippo pathway, are frequently hyperactivated in cancer, where they drive tumor progression and resistance to therapy. Their oncogenic activity relies on interaction with TEAD transcription factors, making the TEAD-YAP/TAZ complex an attractive therapeutic target. Using translational mouse models, we demonstrate that sustained systemic YAP/TAZ depletion leads to severe side effects. However, even transient YAP/TAZ inhibition alone is sufficient to suppress tumor growth in advanced stages. Mechanistically, YAP/TAZ activity promotes T cell exclusion from the tumors by inducing target genes involved in tissue remodeling. Consequentially, YAP/TAZ inhibition induces immune infiltration, but the infiltrating T cells rapidly become exhausted. Combining YAP/TAZ inhibition with immune checkpoint blockade (ICB) overcomes this exhaustion and sensitizes previously resistant tumors to immunotherapy.

cancer biology↗

bioRxiv2025

Influenza A Virus infection is associated with TDP-43 pathology and neuronal damage in the brain

Viral pandemics such as COVID-19 have demonstrated long-term neurological consequences, including memory impairment and depression, emphasizing the importance of understanding virus-brain interactions [1]. Similar concerns have been raised for Influenza A virus (IAV), which has been implicated in neurodegenerative disorders [2, 3]. In this study, we investigated the neuropathological effects of highly pathogenic avian influenza (HPAI) H5N1 and H5N8 strains in a mouse model. Although viral RNA was detected in the brain post-infection, no viral proteins were found, suggesting limited or transient brain replication. Despite this, infected brains showed significant neuronal damage, including axonal loss and nuclear condensation, as evidenced by immunofluorescence and Nissl staining. We also observed pathological changes in TDP-43, including conformational alterations and increased phosphorylation, which required antigen retrieval for detection--features reminiscent of those found in frontotemporal dementia and amyotrophic lateral sclerosis [4, 5]. Transcriptomic analysis further revealed strain-specific host responses, including activation of interferon-related genes and downregulation of microtubule-associated pathways. These findings suggest that IAV infection can trigger hallmarks of neurodegeneration in the absence of persistent viral protein expression, possibly through host-driven mechanisms. Our results underscore the need for further investigation into virus-induced molecular pathways contributing to neurodegenerative disease.

neuroscience↗

bioRxiv2025

Single-Cell and Population-Level Neuromodulation Dynamics in Dual-Electrode Intracortical Stimulation

In neuroprosthetics, intracortical microstimulation (ICMS) recruits cortical networks to evoke brain responses and sensory perceptions. However, multi-electrode ICMS often generates suboptimal percepts compared to single-electrode ICMS, suggesting nonlinear neuromodulation rather than simple summation by multi-electrode ICMS. Yet, the factors and mechanisms underlying this modulation remain poorly understood. To investigate multi-electrode ICMS, we combined two-photon calcium imaging with a well-controlled dual-electrode ICMS in the mouse visual cortex to investigate how neurons integrate converging ICMS inputs at varying intensities. We found that stimulation intensity significantly shapes neuromodulation at both single-cell and population levels. Specifically, low intensities (5-7 {micro}A) have a minimal effect on neural responses. At intermediate intensities (10-15 {micro}A), we observed diverse, nonlinear bipolar modulation--both enhancement and attenuation--at the single-cell level. However, we achieved net enhancement at the population level. At higher intensities (15-20 {micro}A), although the proportion of modulated neurons increased in both enhancement and attenuation directions, the net effect at the population level was neutral (zero modulation). Furthermore, neurons strongly responsive to single-electrode ICMS were more likely to be attenuated, while weaker responding cells exhibited enhanced modulation. The strongest neuromodulatory effects occur at intermediate spatial distances in between the two electrodes. Computational modeling based on spiking neural network composed of adaptive exponential integrate-and-field neurons implicated the importance of inhibitory network dynamics and network variability as key mechanisms. Our experimental data was used to train an advanced deep learning approach, which successfully predicted the neuromodulation patterns induced by dual-electrode ICMS. Our findings reveal intensity- and spatial-dependent rules of neuromodulation by ICMS, providing necessary insights to optimize multi-electrode ICMS for neuroprosthetic applications. Significance statementUnderstanding how cortical neurons integrate concurrent inputs from multi-electrode intracortical microstimulation (ICMS) is essential for advancing neuroprosthetic technologies. We show that dual-electrode ICMS evokes distinct, predictable neuromodulatory effects that depend on (i) stimulation intensity, (ii) a neurons baseline responsiveness to single electrode input, and (iii) its proximity to the electrodes. Low and intermediate intensity dual-electrode ICMS amplifies neural activity compared to single-electrode ICMS, whereas high-intensity stimulation leads to attenuation, limiting net activation.

neuroscience↗

bioRxiv2025

DeepFace: A High-Precision and Scalable Deep Learning Pipeline for Predicting Large-Scale Brain Activity from Facial Dynamics in Mice

We present DeepFace, a next-generation facial analysis pipeline that enhances orofacial tracking and cortical activity prediction in mice. Rather than replacing existing tools, DeepFace builds upon DeepLabCut and Facemap to address scalability bottlenecks and improve behavioral quantification. It offers high precision, keypoint customization, and robust performance across GCaMP6s, GCaMP6f, and jGCaMP8m lines. With scalable batch processing and high-performance computing compatibility, DeepFace enables high-throughput brain-behavior analysis in large-scale preclinical neuroscience.

neuroscience↗