Biology subjects

Chen, N.

Publications and source records attributed to Chen, N..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Species-specific regulation of porcine STING stability and antiviral signaling via its K61 mediated K48 ubiquitination and proteasome degradation

The cGAS-STING pathway has been widely recognized as a critical DNA-sensing pathway that plays a broad-spectrum antiviral role. Livestock, especially pigs, represents one of the most important meat sources. In this study, we identified a key lysine 61 (K61) of porcine STING (pSTING) that plays an essential role in its degradation and antiviral signaling in a species-specific manner, with K61 as the major lysine of pSTING for K48-linked ubiquitination. After virus infection, pSTING recruits the E3 ligase, RNF5, which specifically assembles a K48-linked ubiquitin chain at K61, thereby mediating pSTING proteasomal degradation and reducing its antiviral activity. Meanwhile, the deubiquitylation of K61 is mediated mainly by deubiquitinase USP20, which enhances the stability and antiviral activity of pSTING. Together, given the relatively few lysine numbers in livestock STINGs and species-specific K61 regulation of pSTING stability and antiviral function, the K61 and its specific regulatory enzymes of pSTING could serve as potential targets for breeding of antiviral pigs and design of antiviral drugs, respectively.

immunology↗

bioRxiv2026

Experience-driven reallocation of sensory and mnemonic representations during working memory

Mastering fine perceptual skills requires maintaining precise visual information while simultaneously processing new inputs. In the visual cortex, sensory and mnemonic representations coexist through region-wide multiplexing, yet how perceptual experience reshapes these neural codes remains unknown. Here, combining five days of intensive perceptual training with fMRI and multivariate pattern analyses, we tracked how perceptual learning reformats mnemonic neural representations in a motion-direction discrimination task. Learning improved motion-direction discrimination sensitivity and reshaped the distribution of sensory- and mnemonic-format codes across the visual hierarchy. Sensory-format maintenance was enhanced in V1, and the magnitude of this enhancement closely tracked the behavioral learning effect across individuals, whereas mnemonic-format coding was reduced in V3A. Within V1, learning further increased temporal coupling between sensory and mnemonic codes while leaving their near-orthogonal coding geometry largely unchanged. Our results suggest that perceptual learning reformats working memory codes along a reverse visual hierarchy, strengthening high-fidelity sensory-like representations while preserving the separable organization of multiplexed codes. These findings identify reverse-hierarchy reformatting as a hallmark of experience-driven working memory plasticity.

neuroscience↗

bioRxiv2026

Learning the All-Atom Equilibrium Distribution of Biomolecular Interactions at Scale

Biomolecular functions are governed by dynamic conformational ensembles rather than static structures. While models like AlphaFold have revolutionized static structure prediction, accurately capturing the equilibrium distribution of all-atom biomolecular interactions remains a significant challenge due to the high computational cost of molecular dynamics (MD). We present AnewSampling, a transferable generative foundation framework designed for the high-fidelity sampling of all-atom equilibrium distributions, which is the first model to faithfully reproduce MD at the all-atom level. It uses a quotient-space generative framework to ensure mathematical consistency and leverages the largest self-curated database of protein-ligand trajectories to date, with over 15 million conformations. Statistically, AnewSampling consistently outperforms all prior generative methods on the ATLAS monomer benchmark, and the all-atom capabilities of AnewSampling enable close statistical alignment with ground-truth MD for evaluating atomic biomolecular interactions in protein-ligand dynamics. Furthermore, AnewSampling successfully recovers coupled ligand and side-chain motions in CDK2 systems, overcoming a major sampling hurdle inherent to conventional MD. AnewSampling enables rapid exploration of conformational landscapes prior to intensive simulations, elucidating fundamental biophysical mechanisms and accelerating the broader design of functional biomolecules.

bioinformatics↗

bioRxiv2026

Contrastive learning for antibody-antigen sequence-to-specificity prediction

Predicting which antibodies bind to which antigens directly from primary amino acid sequences remains a major challenge, as no current method can reliably determine this specificity at both a repertoire and proteome scale. Structure-based protein design frameworks can propose antibody binders to specified antigenic epitopes, but they do not solve the "sequence-to-specificity" task of mapping antibodies to cognate epitopes, and vice versa. Here, we introduce CALM (Cross-attention Adaptive Immune Receptor-Antigen Language Model), a dual-encoder plus cross-attentive decoder architecture that treats antibody-antigen recognition as molecular translation. Using contrastive learning, antigen and antibody encoders learn a shared embedding space that aligns cognate epitope-paratope binding pairs. CALM-1.0 is trained and evaluated on 4,138 curated antibody-antigen pairs obtained from the PDB-derived structural antibody database (SAbDab). On a leakage-controlled test split drawn from sequence clusters at 80% identity and unseen during training, CALM-1.0 achieves a mean top-1 retrieval (R@1) of 7%, with consistent performance across both directions (Ab[->]Ag and Ag[->]Ab). CALM establishes a foundation for bidirectional antibody-antigen sequence-to-specificity prediction with the potential to unify retrieval and generative design.

immunology↗

bioRxiv2026

Tirzepatide improves pancreatic β-cell function in mice and patients with type 2 diabetes.

The dual incretin receptor agonist tirzepatide improves {beta}-cell function in T2D patients, but the underlying mechanism remains unclear. This study aimed to elucidate the molecular pathway through which tirzepatide restores {beta}-cell functional improvement. High-fat diet (HFD)-fed C57BL/6J mice were treated with vehicle, a GIP analogue, semaglutide or tirzepatide. Tirzepatide significantly reduced body weight and improved glucose tolerance in HFD-fed mice without altering {beta}-cell mass, proliferation, or apoptosis. Instead, tirzepatide reversed {beta}-cell dedifferentiation, as indicated by reduced ALDH1A3 expression and restored levels of the identity transcription factors PDX1 and MAFA. Single-cell RNA sequencing (scRNA seq) and in vitro studies revealed that tirzepatide up-regulated FOXO1, reactivating the FOXO1-PDX1/MAFA axis. In T2D patients, tirzepatide improved glycemic control, reduced insulin demand, increased HOMA-{beta}, and decreased HOMA-IR. Improvement in HOMA-{beta} correlated positively with baseline insulin resistance. Hence, our study suggested that tirzepatide restores {beta}-cell function in T2D by reprogramming stressed {beta} cells and re-establishing {beta}-cell identity through FOXO1-dependent transcriptional reactivation. These findings provide a mechanistic basis for the superior efficacy of dual incretin receptor agonism in T2D management. ARTICLE HIGHLIGHTSO_LITirzepatide restores {beta} cell identity and function without altering {beta} cell mass in HFD induced diabetic mice. C_LIO_LITirzepatide reverses {beta}-cell dedifferentiation and restores key {beta}-cell transcription factors (PDX1, MAFA) through reactivation of the AKT-FOXO1 signaling pathway. C_LIO_LITirzepatide increases HOMA-{beta} and decreases HOMA-IR in T2D patients, and improvements in HOMA-{beta} positively correlate with baseline insulin resistance. C_LIO_LIThese results demonstrate that tirzepatides therapeutic benefits are not only metabolic but also involve direct restoration of {beta}-cell identity and function. This highlights {beta}-cell reprogramming as a novel therapeutic avenue, thus supporting the broader clinical adoption of dual incretin receptor agonists. C_LI

physiology↗

bioRxiv2026

Network Modulation Enables 3D-Printed Citrate-Based Polymer Scaffolds with Broadly Tunable Mechanical Performance for Regenerative Engineering

Biomaterials with highly tunable mechanical properties and tissue-mimetic structural features are critical for diverse biomedical applications. Photopolymerizable citrate-based polymers (CBP), such as methacrylate polydiolcitrate (mPDC), enable high-resolution fabrication of biodegradable scaffolds via light-based 3D printing for regenerative engineering. However, mPDC scaffolds typically exhibits substantial brittleness due to the formation of highly crosslinked and heterogeneous polymer network, an intrinsic limitation of many acrylate-based polymers, thereby restricting their use across a broad range of tissue types. Herein, we report facile network-engineering strategies to modulate crosslinking density and network topology of CBPs through the incorporation of acrylate-based reactive diluents and/or a thiol-based chain transfer agent, 3,6-dioxa-1,8-octanedithiol (DOD). These approaches enabled significantly improved and broadly tunable mechanical properties, with Youngs modulus spanning 6.8-134 MPa, ultimate tensile strength ranging from 1.8 MPa to 18 MPa, and strain at break varying from 14% to 61%. Notably, incorporation of isobornyl acrylate (IBOA) alone significantly enhanced toughness, yielding a 3.6-fold increase in Youngs modulus (50 MPa vs. 14 MPa) and a 2.8-fold increase in strain at break (39% vs. 14%). Moreover, combined incorporation of IBOA and DOD remarkably improved ductility, achieving a 4-fold increase in strain at break to 61% while maintaining comparable stiffness. All mPDC composites exhibited tunable biodegradability, good cytocompatibility, and excellent 3D printability. Using these composite inks, 3D-printed meniscus scaffolds supported the human chondrocyte growth and fibrochondrogenic matrix deposition, while 3D-printed vascular stents supported endothelial monolayer formation. Collectively, this study establishes a versatile photopolymerizable citrate-based biomaterial platform with broadly tunable mechanical performance, controllable biodegradability, good cytocompatibility, and high printability, offering strong potential for customized biomedical applications ranging from load-bearing to soft tissue engineering.

bioengineering↗

bioRxiv2026

Engineered probiotics for tumor-targeted combination chemoimmunotherapy

Achieving tumor-specific delivery and sustained activation of both cytotoxic and immune-modulating agents remains a critical challenge in chemoimmunotherapy. Here, we present a bacterial platform engineered to combine enzyme/prodrug chemotherapy with immunotherapy, where tumor-homing E. coli Nissle 1917 expresses cytosine deaminase to convert the prodrug 5-fluorocytosine into the cytotoxic drug 5-fluorouracil within tumors. Concurrently, the engineered bacteria produce an IL-15 superagonist and a PD-L1 blocking nanobody to mitigate the immunosuppressive effects of tumor-localized chemotherapy. This platform demonstrated potent antitumor effects in the murine MC38 solid tumor model. Mechanistic studies showed that the combination therapy enhances activation of antigen-presenting cells, T cells and natural killer cells, while reducing immunosuppressive populations. In summary, our approach integrates enzyme/prodrug therapy and immunotherapy into a single bacterial delivery system, overcoming the limitations of conventional therapies and offering a scalable and precision-engineered strategy with an improved safety profile for synergistic cancer treatment. One Sentence SummaryA precision-engineered bacterial platform integrates enzyme/prodrug chemotherapy and immunotherapy to drive synergistic antitumor responses with enhanced safety, offering promise for clinical translation.

cancer biology↗

bioRxiv2026

Nanobody MET CAR T cells show efficacy in solid tumors

BackgroundMET overexpression is associated with poor prognosis in many solid tumors due to its central role in tumor survival, invasion, metastasis, and chemoresistance. While targeting MET with antibody-drug conjugates has shown promising results, engineered cellular immunotherapeutic approaches have not been extensively explored. Compared to conventional single-chain variable fragments (scFv), naturally occurring single-domain antibodies consisting of variable heavy chains only (VHH or nanobodies) are smaller, retain high specificity, and exhibit remarkable biochemical stability. In this study, we tested the efficacy of MET-targeting VHH-CAR-T (chimeric antigen receptor T cells). MethodsWe generated a panel of VHH-CAR-Ts using mRNA electroporation. VHH-CAR-T cells were evaluated in functional assays including cell binding avidity, cytokine production profiles, hydrogel microwell-based cellular kinetics, and in vitro cytotoxicity. We also assessed the therapeutic efficacy of VHH-CAR-T in an in vivo mouse model of metastatic triple negative breast cancer (TNBC). ResultsAmong the tested VHH, we identified those with intermediate avidity as most effective for in vitro tumor killing. VHH-CAR-Ts with CD28 costimulatory domains demonstrated augmented cytotoxicity with favorable selectivity, requiring a minimum antigen density threshold for activation. Mechanistically, VHH-CAR-Ts demonstrated low tonic signaling, high avidity, potent cytokine production, and rapid tumor killing kinetics. When administered in an mRNA format, VHH-CAR-Ts exhibited potent and prolonged control of tumor growth in an in vivo metastatic model of TNBC. ConclusionTaken together, these results demonstrate that VHH-CAR-Ts exhibit robust MET specificity and potent therapeutic efficacy both in vitro and in vivo. Thus, VHH-CAR-T cell therapy represents a promising immunotherapeutic strategy for targeting MET-overexpressing solid tumors. What is already known on this topicMET signaling is an important contributor to the aggressiveness of many solid tumors, and targeting MET by antibody-drug conjugates has shown efficacy and safety. Targeting MET by CAR-T cells has been under study, though with limited potency. What this study addsThis study is the first to demonstrate effectiveness of anti-MET VHH-CAR-T cells. Compared with other antigen binding domains, VHH-incorporated CAR-T cells show low tonic signaling, a favorable cytokine profile, and potent tumor killing. How this study might affect research, practice or policyWith the multiple advantages of VHHs including small size, stability, and low potential for tonic signaling, VHH-CAR-T cells represent a promising approach for CAR-T design against solid tumors.

immunology↗

bioRxiv2026

Biodistribution of mRNA vaccines in rats: Enrichment in injection site and lymph tissues and rapid clearance without tissue persistence

Messenger RNA (mRNA) vaccines using lipid nanoparticles (LNPs) are well-established and globally approved with acceptable safety profiles for preventing respiratory disease. Other mRNA-LNP product concepts are also emerging as novel treatments for broader clinical use. Here, we describe mRNA-LNP vaccine tissue distribution and kinetics after intramuscular dosing using three products formulated with same LNP matrix: mRNA-1273 (Spikevax), mRNA-1647 (a candidate cytomegalovirus [CMV] vaccine), and a reporter mRNA (nascent peptide-luciferase) drug product. Consistent biodistribution patterns were observed across studies: tissues with highest exposures were the injection site, draining lymph nodes, and spleen, with minimal distribution to non-lymphoid tissues. Vaccine components cleared rapidly from circulation and tissues, with complete elimination simulated to occur by [~]2 weeks. Following mRNA-1273 vaccination, Spike protein levels were transiently observed (elimination <5 days) and did not accumulate with repeated dosing. The ionizable lipid in the LNP matrix, Lipid H, underwent biotransformation and was excreted renally and hepatically, with no human-specific metabolites. Collectively, these results indicate that the LNP composition, not mRNA cargo, governs biodistribution. Furthermore, in a SARS-CoV-2 infection-free model, there was no evidence of Spike protein persistence. Overall, the data establish a framework that justifies leveraging biodistribution data across products and supports eliminating redundant animal studies.

pharmacology and toxicology↗

bioRxiv2026

TRPV4 Inhibition by a Natural Product Mediates Analgesia

The transient receptor potential vanilloid 4 (TRPV4) channel, a polymodal calcium-permeable cation channel, is activated by diverse stimuli, including hyposmolarity, moderate heat, mechanical stress, and acidic pH. TRPV4 plays a critical role in the onset and progression of pain and is implicated in multiple pathological conditions, positioning it as an attractive therapeutic target. However, the development of TRPV4-targeted therapeutics has been hindered by limited mechanistic understanding of its inhibition. Here, the natural product (R)-1-(3-ethylphenyl)ethane-1,2-diol (AH001) is identified as a potent, subtype-selective TRPV4 inhibitor. A potential gating mechanism of TRPV4 inhibition is proposed through a combination of structural analyses and site-directed mutagenesis. Electrophysiological studies and cryo-electron microscopy (cryo-EM) further reveal that AH001s glucuronide metabolite, AHP, retains robust TRPV4 inhibitory activity, providing a critical structural basis for rational optimization of AH001 as a lead compound. Notably, AH001 demonstrated significant efficacy in reducing neuronal hyperexcitability in dorsal root ganglia (DRGs) and produced pronounced analgesic effects across multiple pain models, highlighting its therapeutic potential in pain relief. This study offers critical structural and mechanistic insights into TRPV4 inhibition and lays the groundwork for the structure-based design of TRPV4-targeted therapeutics.

biochemistry↗

bioRxiv2025

Chicken IRF10 suppresses the cGAS-STING-IFN antiviral signaling pathway by targeting IRF7

The chicken (ch) innate immune cGAS-STING-IFN signaling pathway plays a crucial role in host antiviral defense, wherein chIRF7 serves as the key downstream transcription factor of chSTING responsible for initiating type I IFN transcription. While chicken IRF family encompasses 8 members, the potential involvement of other IRF members in chicken cGAS-STING-IFN signaling transduction and/or regulation remains poorly characterized. In this study, we identified chIRF10 as a potent suppressor of chicken cGAS-STING-IFN signaling against several viruses, by screening of chIRF family members. Mechanistically, the inhibitory activity of chIRF10 depended on its IRF associated domain (IAD) but not its DNA binding domain (DBD). Further, chIRF10 suppressed both cGAS-STING mediated IFN signaling and TBK1/IKK{varepsilon}/IRF7 activated IFN signaling. Importantly, chIRF10 could interact with chIRF7, and inhibit its dimerization and activation. In summary, our findings unveiled a novel function of chIRF10 as well as a novel regulatory mechanism governing chicken cGAS-STING-IFN antiviral signaling, thereby providing a scientific foundation for developing strategies against chicken viral diseases.

immunology↗

bioRxiv2025

Activity drives local CaMKII synthesis and subcellular localization via autophosphorylation-dependent pathways

Strong repeated stimulation of a neuron triggers an increase in local protein synthesis along with a change in localization of proteins, allowing the neuron to rapidly adjust its proteome in response to activity. One of these proteins, calcium/calmodulin-dependent protein kinase II (CaMKII), is involved in mediating structural and functional changes after activity. While postsynaptic CaMKII translation has been studied, very little is known about presynaptic synthesis, including its mechanisms and the functional consequences. We utilized the Drosophila larval neuromuscular junction (NMJ) as a model to study the molecular requirements for activity-dependent synthesis along with the localization of CaMKII protein. Presynaptic-specific tagging of endogenous CaMKII demonstrates that spaced stimulation rapidly increases presynaptic CaMKII through local translation of pre-existing mRNA, independently of somatic factors. This activity-dependent synthesis requires the distal 3' untranslated region (3'UTR) of the CaMKII mRNA, which is also necessary for steady-state synaptic accumulation. Additionally, we show that activity-dependent synthesis requires CaMKII T287 autophosphorylation-induced activation of the PI3K/Akt/mTor pathway. While activity-dependent redistribution of CaMKII has been previously identified, very little is known about how local synthesis and translocation may interact to define different pools of protein that may have distinct functions. We demonstrate that CaMKII with a T287D phosphomimetic mutant localizes to the synaptic membrane and pulse-chase experiments show that the localization of newly-synthesized CaMKII differs from pre-existing CaMKII, indicating neuronal activity generates spatially distinct, and likely functionally distinct, CaMKII populations which may underlie long-lasting plasticity. Significance StatementSustained synaptic changes after periods of neuronal activity require precise regulation of local protein synthesis. However, the mechanisms that control presynaptic synthesis are poorly understood. We demonstrate that spaced stimulation induces 3UTR-dependent local translation of CaMKII, a key regulator of learning and memory. Additionally, synthesis of CaMKII requires phosphorylation of CaMKII itself, and activation of the PI3K/Akt/mTor pathway. Newly-synthesized and pre-existing pools of CaMKII occupy distinct regions of the bouton, suggesting that new and old CaMKII pools may have specialized functions. These findings illustrate how neuronal activity induces local protein signaling to adjust both the quantity and spatial distribution of CaMKII protein, which has lasting effects on synaptic structure and function.

neuroscience↗

bioRxiv2025

Protofibril Binding Peptides Recognize and Inhibit Huntingtin Amyloid Formation in vitro and in vivo

In Huntingtons disease, polyglutamine expansion in huntingtin exon 1 (Httex1) results in stepwise misfolding, amyloid formation, and neuronal death. Here we used mRNA display directed evolution to generate peptide ligands targeting Httex1 protofibrils, an early, toxic misfolding intermediate. Two distinct peptide families bind protofibrils, one tryptophan rich and the other glutamine rich, resulting in two predominant peptides HD1 (W-rich) and HD8 (Q-rich). Both peptides bind with high affinity and specificity to the misfolded polyQ structure present in protofibrils, a toxic component that is not recognized by existing huntingtin-directed antibodies. Homo- and heterodimers of HD1 and HD8 bind protofibrils with antibody-like affinity, and potently inhibit aggregation of recombinant and cellular Httex1. The HD8-1 heterodimer can be used like an antibody for immunocytochemistry to identify Httex1 aggregates in transfected cells and in the retina of a Huntingtons disease mouse model system (R6/1). Peptide binding to both in vitro and in vivo Httex1 validates in vitro generated Httex1 protofibrils share the same structural features as Httex1 amyloid from cellular and mammalian disease model systems. Further, HD8-1 protofibril recognition enables direct detection of a pathogenic form of Httex1 (misfolded polyQ) as a disease biomarker. Finally, HD1, HD8, and HD8-1 binding and aggregation inhibition defines the protofibril sites that mediate fibril growth. Overall, our observations support developing protofibril-directed ligands as novel, selective, diagnostics and therapeutics for Huntingtons disease. Significance StatementHuntingtin protein polyQ misfolding plays a central role in Huntingtons disease pathogenesis. We used mRNA display to discover a new class of huntingtin-directed ligands protofibril-binding peptides. Unlike presently available antibodies, these peptides selectively recognize misfolded polyQ region, enable using toxic huntingtin aggregates as disease biomarkers, and block huntingtin aggregation in vitro and in vivo. Protofibril binding peptides may thus assist analysis of huntingtin pathology and provide a starting point for designing protein misfolding inhibitors as Huntingtons disease therapeutics.

biochemistry↗

bioRxiv2025

High-throughput cell-free profiling of SARS-CoV-2 RBD variants enables rapid and quantitative in vitro affinity landscape mapping

SARS-CoV-2 variants continue to threaten public health, necessitating the study of cumulative and epistatic effects of receptor-binding domain (RBD) mutations on antibody evasion. We present a high-throughput platform combining cell-free protein synthesis and microfluidics to quantify the affinity of a large number of RBD triplet mutants covering the evolutionary space between wild-type and Omicron against two therapeutic antibodies and one engineered binder. Using rapid in vitro gene assembly and cell-free synthesis, we expressed 518 RBD variants and obtained 31,740 quantitative affinity measurements to generate three comprehensive binding energy landscapes. This approach enables rapid and large-scale in vitro affinity profiling and machine learning-based predictions, providing a valuable tool for studying emerging variants.

systems biology↗

bioRxiv2025

The use of Artificial Intelligence in Magnetic Resonance Imaging of Epilepsy: A Systematic Review and Meta-Analysis

BackgroundThe application of artificial intelligence (AI)/machine learning (ML) to MRI can be a powerful tool to streamline clinical decision-making, yet variability amongst MRI sequences and algorithms have hindered appropriate assessment of reliability and generalizability. MethodsWe conducted a systematic review and meta-analysis of the ability of current AI/ML models operating on MRI data for: 1) epilepsy diagnosis, 2) temporal lobe epilepsy lateralization, 3) lesion localization, and 4) post-surgical outcome prediction. Searches were conducted across PubMed, Medline, and Embase databases from inception until January 1, 2025. We selected studies that employed AI/ML models trained on any MRI modality to classify at least ten patients across the four main objectives for qualitative assessment, and further included in the meta-analysis if they reported an accuracy rate. The primary outcome of the meta-analysis was the overall accuracy of AI/ML models trained on MRI data. The secondary outcome was the concomitant risk of bias evaluation using PROBAST. FindingsWe identified 158 studies for qualitative evaluation and 127 studies for inclusion in the meta-analysis. AI/ML on multimodal MRI could accurately distinguish epilepsy patients from healthy controls (overall accuracy: 88% [85-90]), lateralize temporal lobe epilepsy (90% [87-93]), localize epileptogenic lesions (82% [74-88]), and predict post-surgical seizure-freedom (83% [78-87]). Overall, a high risk of bias remains in the literature; participant bias remained high across all outcomes (64-87%), as well as predictor (88-100%) and analysis (83-100%) bias. Outcome bias was low only for AI/ML studies predicting post-surgical outcomes. InterpretationOur results support promising accuracy of AI/ML models in epilepsy diagnostics and prognostics but remain highly susceptible to bias in participants, predictors, outcome, and analysis domains which limits current translation to routine clinical practice. We encourage closer interdisciplinary collaboration between clinical and scientific groups to improve validation studies based on thorough study design, analysis, and reporting.

neuroscience↗

bioRxiv2025

YAP1 drives aggressive and therapy resistant state in melanoma through reprogramming the chromatin and regulating immune evasive programs

Despite promising initial results in targeting the RAF-MEK-ERK cascade, resistance to BRAF/MEK inhibitors remains a critical challenge in nearly 50% of melanoma patients. Our study demonstrates that robust YAP1 activation in metastatic melanoma correlates with poor survival and drives transcriptional programs linked to therapeutic resistance. Mechanistically, YAP1 predominantly remodels the chromatin landscape in resistant tumors by partnering with BRD4 and TEAD, creating a permissive transcriptional state that sustains oncogenic signaling. Clinical validation in biopsies from resistant melanoma confirms elevated expression of YAP1 target genes. Furthermore, pharmacological inhibition of BRD4 or TEAD reduces YAP1-driven transcription and reactivates antitumor immunity programs. TEAD specific inhibitors (and not verteporfin which is a highly non-specific inhibitor) synergize with immune checkpoint blockade in in vivo model system by promoting increased CD8 T cell infiltration and prolonged survival in the melanoma mouse model. Collectively, these findings reveal a chromatin-centric vulnerability in BRAF/MEK inhibitor-resistant melanoma and propose TEAD specific inhibitors as a promising dual strategy to overcome resistance and reinvigorate the immune response, offering a novel therapeutic avenue for patients. Resistance to BRAF and MEK inhibitors remains a major obstacle in the treatment of melanoma. Here, we show that elevated YAP1 activity in metastatic melanoma is associated with poor patient survival and drives transcriptional programs that promote therapeutic resistance. Mechanistically, YAP1 cooperates with BRD4 and TEAD to reprogram the chromatin landscape, establishing an oncogenic transcriptional state that sustains resistance. Analysis of patient-derived melanoma biopsies confirms increased expression of YAP1 target genes in resistant tumors. Targeting this epigenetic circuitry using pharmacological inhibitors of BRD4 or TEAD effectively suppresses YAP1-driven transcriptional output and restores antitumor immune activity, as evidenced by enhanced CD8 T cell infiltration and prolonged survival in resistant melanoma models. These effects are further supported by transcriptomic and chromatin accessibility analyses, which reveal reduced expression of immune-suppressive and proliferation-associated gene networks upon TEAD inhibition. Collectively, our findings identify a chromatin-centric mechanism underlying resistance to MAPK-targeted therapy and nominate TEAD inhibition as a promising dual-action strategy to both overcome resistance and re-engage antitumor immunity. This work offers a compelling therapeutic avenue for patients with drug-resistant melanoma.

cancer biology↗

bioRxiv2025

Genome-wide associations of fitness components reveal antagonistic pleiotropy and sexual conflict in the Florida Scrub-Jay

Natural populations often exhibit substantial genetic variation in fitness-related traits, providing the raw material for adaptation. The persistence of high levels of genetic variation in the presence of genetic drift and directional selection has long puzzled evolutionary biologists1-3. Recent studies suggest that antagonistic pleiotropy may play a greater role than previously appreciated, highlighting the need for more empirical studies that consider both sexual antagonism and life-history trade-offs4. Here, we performed a comprehensive assessment of fitness trade-offs within and between sexes in an extensively monitored natural population of Florida Scrub-Jays (Aphelocoma coerulescens)5. We found significant additive genetic variance for female fitness and identified several loci associated with variation in survival, fecundity, and lifetime reproductive success. Many loci associated with multiple fitness components had antagonistic effects, particularly within males. Considering genome-wide polygenic effects, we found multiple genetic trade-offs both within and between sexes, especially when considering different fitness components between sexes. Comparing allele frequency trajectories for putatively pleiotropic loci demonstrated that antagonistic SNPs had smaller allele frequency changes than concordant SNPs. Our fine-scale dissection of fitness components reveals substantial antagonistic pleiotropy that affects short-term evolution, highlighting the importance of antagonistic selection in maintaining genetic variation over short time scales in nature.

evolutionary biology↗

bioRxiv2025

Context-Dependent Fitness Outcomes of Helping in the Cooperatively-Breeding Florida Scrub-Jay (Aphelocoma coerulescens)

Cooperatively breeding species frequently live in family groups of related individuals, with helpers delaying their own reproduction and participating in alloparental care, predator vigilance, and territory defense. It remains challenging to disentangle the roles of the indirect fitness benefits of helping kin and the potential direct fitness benefits helpers receive in the evolution of cooperative breeding. While many studies test for associations between helper relatedness and helping effort, few estimate the realized fitness consequences of helping in relation to these factors. Understanding these fitness outcomes elucidates the selective forces that maintain helping behavior, whether through inclusive fitness gains by helping related individuals or as a means of gaining access to later direct fitness benefits. Using 29 years of extensive demographic data from a closely monitored population of Florida scrub-jays (Aphelocoma coerulescens), we quantified the effect of helpers on breeder survival, offspring survival, and nestling production and how these effects depend on relatedness and sex of helpers. We found that female breeder survival was significantly greater when more helpers were present and that offspring survival was greater when more male helpers were present on small territories. Neither effect of helpers depended on the relatedness between helpers and the individuals they helped. Our results suggest that helping behavior is highly context-dependent and varies based on the potential impact of helping and the direct fitness benefits helpers receive.

ecology↗