Biology subjects

Huang, J.

Publications and source records attributed to Huang, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Characterizing benthic community structure across Western Pacific seamounts to ~5,000 m depth: Implications for conservation

AimSeamounts are key components of deep-sea ecosystems. Yet, their biodiversity patterns and conservation needs remain poorly understood, presenting a critical knowledge gap as they face multiple environmental stressors. Here, we aim to characterize benthic community structure across multiple seamounts along the Kyushu-Palau Ridge (KPR) and identify conservation priorities. LocationPhilippine Sea in the Western Pacific. Major taxa studiedDeep-sea benthos. MethodsWe surveyed six transects (13.3{degrees}N-22.9{degrees}N; 614-5,055 m depth; 165 kilometers in total length) using a towed camera system, yielding 31,342 images and 14,218 identified individuals. Community structure was assessed through species depth-range overlap analysis to distinguish nestedness versus turnover patterns. {beta}-diversity was partitioned into local contributions (LCBD) and species contributions (SCBD) to evaluate site-level uniqueness and species-level influence. Generalized linear mixed models were used to relate LCBD and SCBD to depth, slope, aspect, bathymetric position, and functional traits. ResultsCommunity structures varied among slopes and seamounts. Western, steeper slopes were dominated by nestedness, whereas gentler eastern slopes showed mixed patterns of nestedness and gradual turnover. Sessile species largely exhibited nestedness, while mobile taxa showed mixed structures. LCBD declined with depth overall but increased on north-facing slopes and sites with higher broad-scale bathymetric position. Wide-ranging generalist species, particularly among Echinoidea and Holothuroidea, contributed disproportionately to {beta}-diversity. Main conclusionsSeamount benthic communities along the KPR are structured by interactions between depth, geomorphology, and species ecological breadth. The dominance of nestedness on western slopes suggests that protecting shallow, species-rich habitats could capture much of the biodiversity therein. In contrast, the mixed structures on eastern slopes indicate the need for a hybrid conservation approach that includes both shallow summits and deeper, compositionally distinct zones. Our findings highlight the importance of slope-specific, depth-informed strategies to conserve these vulnerable marine ecosystems.

ecology↗

bioRxiv2026

A minimal kinase-phosphatase system and its lipid substrates self-organize into dynamic patterns

Competing lipid kinases and phosphatases are critical for organizing cellular membranes, but whether a minimal system can autonomously organize proteins and lipids into dynamic spatiotemporal patterns is unknown. Here, we report the in vitro reconstitution of the Legionella phosphatidylinositol (PI) 3-kinase MavQ and PI 3-phosphatase SidP. Together with their lipid substrates, PI and PI 3-phosphate (PI3P), these enzymes form a minimal self-organizing system that generates ATP-dependent spatiotemporal patterns, including traveling waves, on model membranes. These behaviors arise from MavQs cooperative membrane binding, SidPs phosphatase activity, and the continual interconversion and redistribution of PI and PI3P within a conserved membrane pool. A reaction-diffusion model reproduces the observed dynamics and predicts that lipid conservation prevents patterns from propagating across membrane discontinuities, which we verify experimentally. Together, these findings establish enzymatic modification of membrane lipids as a distinct molecular strategy for biological pattern formation.

biophysics↗

bioRxiv2026

The Live Concert of Brains: Performer-Audience Neural Coupling Links Ensemble Coordination to Shared Audience Integration

Collective social events often require coordinated action by one group to become shared experience in another, yet how this transformation is organized across multiple brains remains unclear. Live music provides a tractable model of this problem because ensemble coordination, performer-audience alignment, and shared audience integration unfold within the same event. Here we tested whether performer-audience neural coupling acts as a cross-role neural interface linking ensemble coordination to shared audience integration. We recorded brain activity from a nine-person live performance system, consisting of a fixed three-performer ensemble and four independent audience groups, using synchronized multi-device functional near-infrared spectroscopy hyperscanning across live trio performance sessions. Inter-brain neural coupling was analyzed across three relational layers: performer-performer (PP), performer-audience (PA), and audience-audience (AA) coupling. Behavioral ratings showed strong affective engagement and shared evaluative alignment. Neural coupling during live performance was not expressed as a diffuse increase across channel pairs, but was organized into task-sensitive relational components with interpretable PC-corr network modules. Crucially, path-based mediation analyses revealed that PA components statistically bridged PP coordination and AA coupling, yielding multiple complete and partial PP [->] PA [->] AA pathways. Brain-behavior analyses further suggested that mediation-related PA components were linked to shared performance evaluation and emotional alignment. These findings identify performer-audience coupling as a cross-role neural interface through which coordinated production becomes linked to shared collective reception. Significant StatementHow coordinated actions become shared experiences is a major problem in social neuroscience, yet most studies examine pairs of people. Using live music as a model of group interaction, we found that brain-to-brain alignment was organized across social roles rather than arising as a uniform response to the same event. Performer-audience alignment occupied a bridging position between coordination within the ensemble and integration within the audience. This identifies a systems-level architecture through which collective action may become linked to collective experience. The framework moves multi-brain research beyond dyads and offers a general approach for studying classrooms, public speaking, theater, rituals, and team events, where one group generates structured behavior that another group jointly receives and interprets.

neuroscience↗

bioRxiv2026

Microbial Metabolites Potentiate MAIT Cell Anti-Tumor Immunity Against Solid Tumors

Mucosal-associated invariant T (MAIT) cells sense riboflavin metabolites through the monomorphic antigen-presenting molecule MR1, providing a unique opportunity to therapeutically mobilize a broadly shared T cell population without genetic engineering. Here, we show that the highly potent microbial metabolites, 5-OP-RU and 5-OE-RU, can be exploited as pharmacologic precision immune activators to drive human MAIT cell responses against solid tumors. Ligand stimulation in human co-culture systems elicited robust MAIT cell cytotoxicity, inflammatory cytokine secretion, and transcriptional states transformation. In vivo administration of riboflavin ligands 5-OP-RU significantly suppressed tumor growth in xenograft liver cancer models. Metabolite-driven MAIT activation also reprogrammed the local immune landscape, enhancing effector function and overcoming features of the immunosuppressive niche by markedly eliminating tumor-associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs) within the tumor microenvironment (TME). These findings reveal that microbial riboflavin metabolites can power and redirect MAIT cells to solid tumors, establishing MR1-metabolite signaling as a tractable therapeutic axis for liver cancer and other solid malignancies.

cancer biology↗

bioRxiv2026

Ribonucleotide Reductase Inhibition Overcomes FLT3 Inhibitor Resistance in Acute Myeloid Leukemia

Internal tandem duplication mutations in FLT3 (FLT3ITD) occur in approximately 30% of patients with acute myeloid leukemia (AML) and are among the most common genetic alterations in this disease. FLT3ITD is a major driver of AML and is associated with poor clinical outcomes. Although FLT3 inhibitors (FLT3is) have significantly improved outcomes for patients with FLT3ITD+ AML, acquired resistance remains a major barrier to durable clinical benefit. Reactivation of RAS/MAPK signaling, often driven by activating NRAS mutations, is a major mechanism of FLT3i resistance in AML; however, effective strategies to overcome this resistance remain lacking. Here, we identify ribonucleotide reductase (RNR) as a critical therapeutic vulnerability in NRAS-driven FLT3i-resistant FLT3ITD+ AML. Activation of RAS signaling through SPRY3 loss or oncogenic NRAS mutations confers robust resistance to FLT3is, whereas pharmacologic inhibition of RNR with multiple inhibitors, as well as siRNA-mediated RNR suppression, reverses FLT3i resistance and restores FLT3i sensitivity across multiple FLT3ITD+ AML models in vitro. In vivo, clofarabine, an FDA-approved RNR inhibitor (RNRi), significantly overcomes NRAS mutation-driven FLT3i resistance. In combination with FLT3 inhibition, clofarabine markedly suppresses the progression of FLT3i-resistant AML and significantly prolongs survival in cell line-derived xenograft (CDX) models. Importantly, the therapeutic efficacy of the gilteritinib/clofarabine combination was independently validated in two genetically distinct patient-derived xenograft (PDX) models harboring different NRAS mutations, demonstrating robust reduction of leukemia burden and confirming the generalizability of RNR inhibition in primary FLT3i-resistant AML. Together, these findings identify a previously unrecognized therapeutic vulnerability in FLT3i-resistant FLT3mut+ AML and establish RNR inhibition as an effective strategy to overcome FLT3i resistance, providing a strong rationale for the clinical evaluation of RNRis in combination with FLT3is in patients with resistant AML. SignificanceAlthough FLT3 inhibitors (FLT3i) are an important therapeutic advance in FLT3ITD+ AML, resistance commonly develops. We identified ribonucleotide reductase (RNR) as a new key vulnerability in NRAS-driven FLT3i-resistant AML and demonstrated that multiple RNRis, including the FDA-approved agent clofarabine, restore FLT3i sensitivity and enhance antileukemic activity, supporting a clinically actionable combination strategy.

cancer biology↗

bioRxiv2026

ER Stress-Response Signaling Regulates Chamber-Specific Growth between Right and Left Ventricles during Postnatal Development.

BackgroundDifferential growth between the left (LV) and right ventricles (RV) is a cornerstone of normal heart morphogenesis after birth, leading to the relatively larger and dominant LV over RV in the adult heart regarding size and function. Yet, little is known about the factors that regulate this chamber-specific growth. MethodsWe used both loss-and gain-of-function mouse models, achieved through genetic or pharmacological manipulation of IRE1 or Xbp1 in cardiomyocytes. We also used primary cultured neonatal cardiomyocytes to explore the roles of IRE1, spliced Xbp1 (sXbp1: activated form), and newly identified sXbp1 downstream targets. In addition, we generated heart-specific mosaic mutant mouse models using CRISPR/Cas9/AAV9-based somatic mutagenesis to elucidate the roles of sXbp1 downstream targets in cardiomyocytes. ResultsPharmacological inactivation of IRE1 and genetic depletion of Xbp1 resulted in a smaller LV size, due to decreased cardiomyocyte proliferation and hypertrophic growth, as well as increased cardiomyocyte death. These effects were not observed in the RV. Cardiomyocyte-specific induction of IRE1 or sXbp1 led to increased ventricular size in both ventricles, through enhanced cardiomyocyte proliferation and hypertrophic growth in both LV and RV, and reduced apoptosis in the RV. We identified two ER resident transmembrane proteins, Vimp and Rpn2, as direct binding partners of sXbp1 in targeted gene regulation at the chromatin level. CRISPR/Cas9/AAV9-based somatic mutagenesis mouse models for Vimp and Rpn2 revealed that both genes regulate cardiomyocyte proliferation, hypertrophic growth, and death. We also observed accumulated misfolded proteins in these two mutant hearts. Conclusions We demonstrate that the IRE1-Xbp1-Vimp/Rpn2 axis regulates differential ventricular size between LV and RV during postnatal development by orchestrating cardiomyocyte proliferation, hypertrophic growth, and death through regulating protein homeostasis. Clinical PerspectiveO_ST_ABSWhat Is NewC_ST_ABSO_LIIRE1-Xbp1 axis is dominantly activated in the LV cardiomyocyte during the postnatal period in mouse heart. C_LIO_LIIRE1-Xbp1 mediated ER stress signaling increases cardiomyocyte proliferation and hypertrophic growth and decreases apoptosis in the postnatal period. C_LIO_LIActivated Xbp1 directly regulates LV-specific cardiomyocyte protein homeostasis via interaction with ER membrane targeted Vimp and Rpn2. C_LI What Are the Clinical Implications?O_LIDifferential heart growth patterns between the LV and RV are critical for normal morphogenesis and function of each ventricle. C_LIO_LIControl of protein homeostasis by modulating ER stress signaling could be a potential therapeutic approach for single-chamber heart diseases. C_LI

developmental biology↗

bioRxiv2026

Plaque-associated oligodendrocyte proteostatic failure underlies myelin loss in Alzheimers disease

Alzheimers disease (AD) features amyloid-{beta} plaques and tau pathology, yet the mechanism underlying early and clinically significant myelin loss remains unresolved. Here, we report human iPSC-derived forebrain organoids with doxycycline-inducible expression of SOX10, OLIG2, and NKX6-2 (SON), which generate robust, mature oligodendrocytes and compact myelin in vitro and in vivo. Introducing amyloid precursor protein (APP) pathogenic mutations produces extracellular amyloid-{beta} plaques and phosphorylated tau, accompanied by reduced myelin basic protein (MBP) expression and disrupted myelin ultrastructure. Single-cell and spatial transcriptomics combined with amyloid plaque imaging reveal that oligodendrocytes in plaque-dense regions show pathological changes in calcium signaling, immune activation, lipid remodeling, and protein catabolic pathways. Notably, MBP protein is reduced despite elevated myelin-related transcription, suggesting plaque-induced degradation of myelin proteins. Consistent with this, proteasomal inhibition restores MBP protein levels and improves compact myelin ultrastructure in AD organoids. In human AD brain tissue, protein catabolic pathways are similarly upregulated with increasing plaque density. Together, these findings identify plaque-associated oligodendrocyte proteostatic failure as a candidate mechanism of myelin loss and a potential therapeutic pathway in AD.

neuroscience↗

bioRxiv2026

Bone Mechanosensing Dictates Hematopoietic Stem Cell Fate and Immune Homeostasis

The vertebrate water-to-land transition was accompanied by a six-fold increase in gravitational force, followed by the migration of hematopoietic stem cells (HSCs) from kidney or liver to the bone marrow, and the acquisition of enhanced immune functions to cope with novel environmental pressures. Bone senses mechanical loading and provides a microenvironment for HSC development, yet whether bone mechanosensation affects immune cell development and immune homeostasis remains unclear. Here, we unveil bone as a mechanosensory organ that translates mechanical force into hematopoietic instructions. Mechanical loading of bone directs HSCs toward lymphoid lineages in mice and non-human primates, whereas unloading favors myeloid commitment. This process requires osteocyte mechanosensor Piezo1, which induces loading-responsive bone-derived factors such as IL1R2, SERPINC1 and INMT, thereby restraining inflammatory signaling and guiding HSC differentiation. Osteocyte Piezo1 deficiency recapitulates the hematopoietic and immune alterations observed during unloading. Functionally, this pathway enhances acute infection resistance and suppresses immunosenescence in mice and in aged long-tailed macaques. Notably, skeletal mechanoregulation of immune homeostasis is conserved across vertebrate species. Our research defines the mechano-bone-immune axis (mechano-osteoimmunology), offering a novel evolutionary perspective on the interconnected development of the skeletal and immune systems and presenting a promising non-pharmacological target to address immune dysfunction.

immunology↗

bioRxiv2026

CatESO: Differentiable Enzyme Sequence Optimization Guided by Substrate-Aware kcat Prediction

Enzymes drive biological chemistry and offer greener routes to chemicals, materials and medicines, yet their broader use as biocatalysts is often limited by insufficient catalytic turnover. Improving turnover is hard: measured rate constants are scarce and protein sequence space is vast. Deep-learning models now predict the turnover number, kcat, with growing accuracy, but they are typically applied after sequence generation to score or filter candidates, which separates the kinetic objective from the design itself. To bridge the gap between sequence generation and kinetic evaluation, we introduce CatESO, a differentiable sequence optimizer that enables direct, gradient-guided design of substrate-specific catalytic turnover. By backpropagating through a cross-modal kcat predictor under continuous sequence relaxation, CatESO co-optimizes predicted catalytic activity, evolutionary plausibility and structural integrity in one end-to-end framework, using ESM-2 and ESMFold to keep designs evolutionarily plausible and foldable. Across seven stringent out-of-distribution enzymes spanning EC classes 1-7, CatESO raised model-predicted kcat for the vast majority of designs, with a median predicted fold change of 1.52 while every variant retained a pLDDT above 70. Against RFdiffusion3-LigandMPNN pipeline and ZymCtrl, CatESO struck a better balance between predicted activity and structural confidence. By making substrate-conditioned kinetic objectives differentiable, CatESO carries differentiable protein design beyond structure- and binding-centred goals to enzyme catalytic function, giving a general route to function-oriented enzyme engineering.

biochemistry↗

bioRxiv2026

METTL1 regulates glioma proliferation through internal m7G methylation of EPHA2

BackgroundMethyltransferase-like 1 (METTL1) is highly expressed in organs like the pancreas but less so in the brain. The METTL1-WDR4 complex catalyzes N7-methylguanosine (m7G) methylation in tRNA, miRNA, mRNA, and rRNA, which impacts RNA stability and function. These modifications affect mRNA translation and tRNA functionality, influencing protein production and cellular activities. Such modifications can regulate tumor growth, invasion, and metabolism by selectively controlling protein expression. MethodGene expression data from public databases were analyzed to compare METTL1 expression in normal and tumor tissues. Western blot (WB) and immunohistochemistry (IHC) were used to quantify METTL1 levels in glioma samples and assess their prognostic significance. Cell viability, migration, invasion, and proliferation were evaluated using Cell Counting Kit-8 (CCK-8), wound healing, Transwell, cell cycle analysis, and colony formation assays. RNA immunoprecipitation PCR (RIP-PCR) identified m7G methylation sites on EPHA2 mRNA, and RNA stability was assessed with actinomycin D. ResultsBioinformatics analysis revealed that METTL1 is overexpressed in gliomas, correlating with poor prognosis. Knockdown of METTL1 significantly affected cell proliferation, migration, and invasion. RNA sequencing (RNA-seq) and m7G analysis identified EPHA2 as a downstream target, influencing the cell cycle via the AKT pathway. RIP and methylated RNA immunoprecipitation (MeRIP) confirmed two m7G sites on EPHA2 mRNA regulated by METTL1. Small interfering RNA (siRNA)-mediated METTL1 knockdown in EPHA2 mutants affected mRNA stability. Rescue experiments restored cell proliferation and AKT pathway gene expression. ConclusionMETTL1 methylates EPHA2 mRNA, enhancing its stability and expression, which activates the AKT signaling pathway and influences glioma cell proliferation. METTL1 could be a potential therapeutic target in glioma treatment.

cell biology↗

bioRxiv2026

A Glutamine antagonist-modulated tumor microenvironment unleashes enzalutamides immunotherapeutic effects

Androgen receptor (AR) antagonists, such as enzalutamide, suppress prostate cancer (PCa) cells to achieve temporary therapeutic effects. In addition to tumor cell-autonomous suppressive function, AR antagonists can also potentially exert anti-tumor effects via mitigating cytotoxic T cells exhaustion. However, strategies for effectively harnessing enzalutamides immunotherapeutic effects remain elusive. In studying a recently described glutamine antagonist prodrug (DRP-104) in PCa models, we found that despite the initial response, tumors ultimately became resistant. Intriguingly, compared to the untreated (DRP-104 treatment-naive) tumors, the resistant tumors became highly susceptible to enzalutamide in vivo. Additionally, treating tumors with DRP-104 and enzalutamide simultaneously also yielded superior therapeutic efficacy. We demonstrated that DRP-104 therapy promoted the infiltration of CD8+ T cells as well as regulatory T cells (Treg) in responsive tumors, and the tumor-infiltrating Treg were mostly depleted upon enzalutamide treatments. Mechanistically, we showed that Treg differentiation from mouse CD4+ T cells was attenuated by enzalutamide. We further demonstrated that Treg induction was accompanied by the interaction between AR and aryl hydrocarbon receptor (AhR), the nuclear receptor indispensable for Treg differentiation, in the nuclei of CD4+ T cells, and this interaction was diminished by enzalutamide. In further support of AR signaling in Treg biogenesis, analysis of available gene expression datasets found that AR expression was elevated in Treg when compared to CD4+ T cells in human peripheral blood mononuclear cells (PBMCs). In addition, it was positively correlated with Treg module scores in several human cancer types. Finally, using an anti-GPC3 (Glypican 3) vaccination model, we demonstrated that CD4+ T cells subjected to Treg induction in the presence of enzalutamide were less effective in protecting GPC3-expressing tumor cells from CD8+ T cells cytotoxic killing. Collectively, these results suggest that AR promotes Treg s differentiation and/or immunosuppressive functions, and nominate enzalutamide as a Treg-mitigating agent for potentiating immunotherapies. Our results also demonstrate that an otherwise unintended, Treg-promoting property of DRP-104 can be leveraged to unleash the immune-regulatory function of enzalutamide for the treatment of PCa.

cancer biology↗

bioRxiv2026

AI-enabled rhodopsin design for blue-light enhanced bacterial growth

We developed an AI-guided design pipeline that generated and validated non-natural microbial rhodopsins with spectral properties not yet known in nature. The pipeline comprised a three-stage in silico design, a genetic algorithm (GA) for sequence generation, a stacked LASSO and XGBoost machine-learning (ML) regressor for spectral prediction and fitness ranking, and a Markov-based sequence plausibility filter to enforce proton pumping like characteristics. Four candidate rhodopsins (APR1, APR2, APR6, and APR7) targeting blue light absorption were designed and AlphaFold3 structural modelling predicted retinal binding pocket architecture consistent with outward proton-pumping function. Experimental characterisation confirmed that all four variants absorbed light at [~]410 nm and significantly promoted the growth of Cupriavidus necator under blue light illumination. This study demonstrates that AI-enabled design can engineer proteins with no natural precedent, generating light-harvesting rhodopsins with novel spectral properties while preserving biological function, marking a significant advance in programmable synthetic biology.

Synthetic Biology↗

bioRxiv2026

UTRGen: A unified framework for full-spectrum design of mRNA 5' UTRs

AO_SCPLOWBSTRACTC_SCPLOWThe 5' untranslated region (5' UTR) is a key regulatory element that governs mRNA translation and protein output. However, existing computational methods typically address isolated tasks such as functional prediction or sequence optimization, limiting their ability to support rational design across the full 5' UTR engineering workflow. Here, we present UTRGen, a unified modeling framework for 5' UTRs that integrates sequence generation, multi-property prediction, and constrained function-guided design. UTRGen is pre-trained autoregressively on large-scale 5' UTR datasets from multiple species and subsequently adapted to diverse downstream regulatory tasks. Across systematic evaluations, UTRGen generates novel and diverse 5' UTRs while preserving sequence, structural, and functional characteristics of natural UTRs. After task-specific fine-tuning, UTRGen achieves state-of-the-art performance across 14 benchmark datasets, improving translation efficiency prediction by up to 11.1%, expression level prediction by up to 13.2%, and mean ribosome load prediction by up to 3.0% relative to the strongest baselines. It also achieved the best overall performance for internal ribosome entry site identification. To enable controllable design, we formulate function-guided 5' UTR design as a GRPO-based refinement process over a pre-trained autoregressive sequence prior, using composite rewards to encode functional objectives and biological constraints while regularizing toward the natural 5' UTR distribution. The resulting sequences show consistently improved predicted translation efficiency and expression levels across cellular contexts, and reveal interpretable sequence features associated with high activity, including reduced C content, fewer upstream AUGs, and depletion of inhibitory motifs. Together, our results establish a unified modeling strategy for 5' UTR design and lay a foundation for programmable control of translation.

bioinformatics↗

bioRxiv2026

Targeting Cellular Pseudo-Senescence to Overcome PARP inhibitors Resistance in BRCA1 -Mutated Breast Cancer

Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) are a mainstay therapy for homologous recombination (HR)-deficient cancers; however, resistance remains a major clinical challenge. Previously, through a genome wide CRISPR screen, we identified ZNF251 haploinsufficiency as a novel driver of PARPi resistance. In BRCA1-mutant (BRCA1mut) cells, ZNF251 deficiency led to HR hyperactivation, conferring PARPi resistance that could be reversed by RAD51 inhibition. In this study, we further show that ZNF251 deficiency induces replication stress and a pseudo-senescence state, in which cells exhibit molecular and phenotypic markers of senescence while retaining proliferative capacity. Because senomorphic and senolytic therapies can target senescent cells, we tested whether these approaches could overcome PARPi resistance in ZNF251-deficient breast cancer cells. Critically, targeting this senescence-like state with either senomorphic agents, such as cytokine inhibitors, or senolytic agents, such as BCL-2 and BCL-XL inhibitors, overcame PARPi resistance ex vivo and in vivo. Importantly, pseudo-senescence was also observed in other PARPi-resistant contexts driven by HR hyperactivation, including 53BP1- and Shieldin-mutant cells, suggesting that it may represent a broader mechanism underlying PARPi resistance in breast cancer. Furthermore, in two olaparib-resistant, BRCA-mutant triple-negative breast cancer organoid models, treatment with DT2216, a BCL-XL-targeting PROTAC, sensitized both models to olaparib. Together, our work defines a novel pathway linking HR hyperactivation, replication stress, and pseudo-senescence, and positions both senomorphic and senolytic therapies as promising strategies to overcome PARPi resistance in BRCA1mut breast cancer. HighlightsO_LIZNF251 deficiency drives PARP inhibitor resistance through HR hyperactivation, replication stress, and pseudo-senescence in BRCA1-mutant breast cancer. C_LIO_LISenomorphic and senolytic therapies overcome PARP inhibitor resistance in vitro, in vivo, and in patient-derived organoid models. C_LIO_LIPseudo-senescence represents a shared vulnerability of HR-hyperactivated PARPi-resistant cancers and can be therapeutically targeted. C_LI

Cancer Biology↗

bioRxiv2026

Conspecific Presence Facilitates the Reliable Expression of Nicotine Reward in Juvenile Zebrafish

RationaleAdolescence is a period of heightened vulnerability to nicotine reinforcement. While zebrafish are a valuable model for investigating drug reward, standard conditioned place preference (CPP) assays typically test subjects in isolation. In this highly social species, solitary testing may act as an environmental stressor that confounds behavioral readouts. ObjectivesThis study examined how social context during testing (isolated vs. grouped) affects experimental attrition, behavioral stability, and nicotine CPP expression in late juvenile zebrafish. MethodsZebrafish housed in groups of four were tested either individually (isolated) or in their housing groups (grouped) during daily 20-minute sessions. Following baseline preference assessments, subjects underwent six days of conditioning pairing their initially non-preferred compartment with fish water or nicotine (0.5, 1.6, or 5.0 {micro}mol/L). Place preference, locomotion, and thigmotaxis were assessed on a drug-free test day. ResultsIsolated testing reduced distance traveled, decreased swimming speed, and increased time spent near tank walls, indicating heightened anxiety-like behavior. Experimental attrition was significantly higher in isolated (38.9%) than grouped (2.5%) subjects. Grouped subjects developed significant place preference at 1.6 and 5.0 {micro} mol/L nicotine, whereas preference was not detectable in isolated subjects. ConclusionsSolitary testing acts as a stressor that increases experimental attrition and masks place preference. Conversely, testing in the presence of conspecifics stabilizes behavior and facilitates the detection of nicotine reward in late juvenile zebrafish.

animal behavior and cognition↗

bioRxiv2026

Entanglement-governed protein networks enable mechanically adaptive artificial skin for transplantation-scale skin replacement

Artificial skin substitutes that simultaneously achieve mechanical robustness, regenerative bioactivity, and transplantation-scale tissue integration remain challenging to engineer. Here we report a mechanically adaptive bilayer artificial skin based on entanglement-mediated protein networks. By integrating protein chain entanglement, flexible molecular linkers, and photo-triggered intermolecular crosslinking, we establish a hierarchically organized protein matrix with enhanced toughness, structural adaptability, and regenerative compatibility. Spatial biofunctionalization further enables integration of an antibacterial Zn{superscript 2}-coordinated epidermal layer and a regenerative CLP-EGF-functionalized dermal layer within a unified construct. The engineered skin promotes cellular proliferation through PI3K-AKT-mTOR activation, exhibits sustained antibacterial activity, and supports large-area full-thickness skin replacement covering approximately 40% of the dorsal skin surface in mice. The construct further accelerates diabetic wound repair and extracellular matrix remodeling in vivo. These findings establish entanglement-mediated protein engineering as a strategy for mechanically adaptive regenerative biomaterials and provide a platform for transplantation-scale skin regeneration.

bioengineering↗

bioRxiv2026

Dissecting the sources of variation in neuronally differentiated iPSC lines through multi-omics analysis

Induced pluripotent stem cells (iPSCs) are widely used as patient-specific disease models, yet substantial unexplained variability in molecular and functional readouts limits their reliability. Here, we systematically investigated the sources of variation in iPSC-derived neurons for three rare genetic disorders: Myotonic Dystrophy Type 1, chromodomain-DNA-helicase-binding protein 2-related disorder and N-acetylneuraminic acid synthase deficiency. This was performed by profiling multi-omics layers: genomics, epigenomics, transcriptomics, proteomics, metabolomics and lipidomics. Our study found that clonal variability was comparable to inter-patient differences and that neuronal differentiation state and nutrient-driven metabolic activity emerged as dominant contributors to variability observed across omics layers. Clonal differences could partly be attributed to stochastic differences in DNA methylation established during reprogramming. By modeling and correcting the observed variation, we improved the detection of disease-associated molecular signatures. Our study provides guidelines for improved study design and data analysis to minimize variability, enabling robust biomarker discovery and reliable iPSC-based disease modeling.

cell biology↗

bioRxiv2026

Lack of ancestral SARS-CoV-2 imprinting promotes BA.3.2.2 infection in children

The ongoing evolution of SARS-CoV-2 is heavily constrained by population-level immune imprinting. Recent genomic surveillance reveals an unexpected demographic shift: the highly mutated BA.3.2.2 sublineage is significantly enriched in paediatric populations globally, unlike concurrent variants XFG and NB.1.8.1. Here, the evidence demonstrates that this paediatric susceptibility arises from the absence of ancestral Wuhan-strain immune imprinting. Serological analyses reveal a profound failure to neutralise BA.3.2.2 in young children with no ancestral strain exposure. Concurrently, single-B-cell sequencing analyses demonstrate that BA.3.2.2 completely evades Omicron-specific Class 1/4 neutralising antibodies, encoded by IGHV2-5 and IGHV5-51, which dominate the repertoires of weakly imprinted individuals such as young children. Conversely, BA.3.2.2 remains uniquely susceptible to broadly cross-reactive Class 1 antibodies, encoded by IGHV3-53/66, typically enriched in adults with strong ancestral imprinting, such as mRNA vaccine recipients. Critically, sustained transmission of BA.3.2.2 in paediatric populations may catalyse the emergence of secondary variants that combine the paediatric-evading features of BA.3.2.2 with adult-evading Class 1 mutations. This could allow the lineage to breach the imprinted immunity of the adult population, potentially driving widespread global transmission. Together, these findings show that legacy immune imprinting paradoxically provides superior protection against a highly divergent saltation variant, directly explaining the age-biased transmission of BA.3.2.2, and informing future paediatric vaccination strategies.

immunology↗