Biology subjects

Chen, X.

Publications and source records attributed to Chen, X..

At least 145 records · Page 8Linked to original sources

bioRxiv2026

A Perturb-seq screen guided by species divergence uncovers pathways for collateral artery formation

Collateral arteries are natural bypasses that can reroute blood flow around arterial blockages, limiting tissue injury during stroke and coronary artery disease. Despite their clinical effectiveness, therapeutic strategies to stimulate collateral artery growth remain unavailable due to our limited understanding of their developmental mechanisms. Remarkably, guinea pigs display exceptionally dense collateral artery networks across various organs, resulting in complete resistance to ischemic damage in the brain and heart. In this study, we compared single-cell RNA sequencing (scRNA-seq) from guinea pig and mouse tissues to identify endothelial cell (EC) gene expression patterns associated with extensive collateral artery development. We then developed an in vivo Perturb-seq platform in mice to test whether genes differentially expressed in guinea pigs influence artery EC specification. This pipeline identified artery repressors that were downregulated in guinea pigs and increased pial collateral abundance when inhibited in mice. Downstream analysis suggests that artery repressors, including WNT and hypoxia response genes, function in two capillary EC subsets--Esm1+ pre-artery and Apln+ angiogenic tip cells. Reduced activity of these repressors allows more ECs to acquire arterial identity, potentiating collateral artery formation. Collectively, our study establishes a strategy for discovering the genes underlying species-specific traits, suggests that guinea pigs have collaterals due to decreased activity of artery inhibitor pathways and hypoxia responses, and identifies novel targets for stimulating collateral artery formation (Graphical abstract). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/721711v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@18b36cdorg.highwire.dtl.DTLVardef@bafbaforg.highwire.dtl.DTLVardef@1e1a6bdorg.highwire.dtl.DTLVardef@189f585_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2026

Multidimensional Mechanistic Study of Panax Notoginseng Saponins in the Treatment of Alcohol-Induced Osteonecrosis of the Femoral Head: Integrating Network Pharmacology, Molecular Dynamics Simulation and In Vivo Validation

BackgroundAlcohol-induced osteonecrosis of the femoral head (AIONFH) is an orthopedic disorder from chronic alcohol abuse, characterized by disrupted femoral head blood supply, osteocyte death and structural collapse. Current hip-preserving therapy is unsatisfactory, and most patients eventually require total hip arthroplasty. Panax Notoginseng Saponins (PNS), the core active component of Panax notoginseng, exerts pro-angiogenic and anti-osteocyte apoptosis effects, but its specific therapeutic mechanism remains unclear. ObjectiveThis study used network pharmacology, molecular dynamics simulation and animal experiments to identify PNSs active components, core targets and key pathways for AIONFH, verify its in vivo efficacy, and provide a scientific basis for clinical application. MethodsPNS active components, their targets and AIONFH-related targets were screened from databases; intersection targets constructed an interaction network, core targets were screened by three machine learning algorithms, with concurrent GO and KEGG analysis. Molecular docking was performed between core targets and PNS components; Gromacs 2022 conducted 100 ns simulation to evaluate complex stability. AIONFH rat models were grouped with 4-week intragastric intervention; pathology, immunofluorescence and PCR were used for detection. Results and DiscussionNetwork pharmacology identified 127 PNS targets and 18 intersections with 672 AIONFH targets. Six core targets (including FGF2, HSD11B1) were screened; KEGG indicated VEGF pathway as key. Ginsenoside Re bound HSD11B1 with the lowest binding energy (-12.4 kcal/mol), and 100 ns simulation confirmed complex stability. Animal experiments showed PNS improved trabecular structure and regulated osteocyte activity. PNS treats AIONFH via multi-component, multi-target mode, core mechanism being osteocyte apoptosis inhibition. Results and DiscussionNetwork pharmacology screening identified 127 potential targets of PNS, and 18 potential intersection targets were obtained by overlapping with 672 AIONFH-related targets. Six core targets including FGF2 and HSD11B1 were screened out by machine learning, and KEGG analysis indicated that the VEGF pathway and other pathways were the key signaling pathways for PNS action. Molecular docking showed that Ginsenoside Re had the lowest binding energy with HSD11B1 (-12.4 kcal/mol), and 100 ns molecular dynamics simulation confirmed the stable conformation of this complex. Animal experiments demonstrated that PNS could improve trabecular bone structure and regulate osteocyte activity. In summary, PNS exerts a therapeutic effect on AIONFH through a multi-component, multi-target and multi-pathway mode, with the core mechanism of inhibiting osteocyte apoptosis.

pharmacology and toxicology↗

bioRxiv2026

Tie2 signaling in the tumor microenvironment orchestrates breast cancer cell dissemination through TMEM doorways

During breast cancer metastasis, tumor cells migrate toward intratumoral blood vessels and intravasate through stable structures known as TMEM (Tumor Microenvironment of Metastasis) doorways. TMEM doorways, composed of a Mena-expressing tumor cell, a Tie2hi/VEGFhi macrophage, and an endothelial cell, are clinically validated prognostic markers of distant metastasis in breast cancer and represent the exclusive sites of tumor cell intravasation. We previously demonstrated that Tie2 signaling is essential for TMEM doorway function and tumor cell intravasation. In this study, we investigated how Tie2 signaling promotes tumor cell intravasation and metastasis. Because all three TMEM doorway-associated cell types can express Tie2, we sought to determine which of these cells contribute to the Tie2 signaling-dependent vascular opening at TMEM doorways and tumor cell dissemination. We found that endothelial cells associated with TMEM doorways secrete Ang2, which stimulates VEGF-A expression in Tie2hi macrophages. Elevated VEGF-A levels at TMEM doorways increase vascular permeability, facilitating tumor cell entry into the bloodstream. Using tissue staining and line-scan analysis of Tie2 and lineage markers in human and mouse breast cancer models, we observed Tie2 expression in macrophages, tumor cells, and endothelial cells. To assess functional contributions, we selectively disrupted Tie2 in macrophages, endothelial cells, and cancer cells using CRISPR-Cas9 and RNAi approaches and tested in which of these cell-knockouts of Tie2 expression affected transendothelial migration in vitro. Macrophage-specific Tie2 deletion had the greatest impact on tumor cell intravasation. To confirm this finding in vivo, we generated a mouse model with inducible, macrophage-specific Tie2 knockout. Acute, targeted loss of Tie2 specifically in macrophages significantly reduced TMEM doorway associated vascular opening and tumor cell intravasation. Together, these findings establish macrophage Tie2 signaling as a critical driver of TMEM doorway-mediated vascular permeability and metastatic dissemination in breast cancer.

cancer biology↗

bioRxiv2026

PanVariants: Best Practice for Pangenome-based Variant Calling Pipeline and Framework

BackgroundAlthough pangenome references offer richer population diversity compared to linear references, current mainstream pangenome-based variant callers are limited to detecting only known variants stored in the graph. To address this limitation, we developed PanVariants, a novel pipeline designed to improve the detection of both known and novel variants accurately. We systematically evaluated its performance against the traditional linear alignment solution (BWA+GATK/Manta) and the existing pangenome-aware solution (DRAGEN/PanGenie) in three contexts: small variants (SNVs/indels) and structural variants (SVs) accuracy in Genome in a Bottle samples, clinical detection on positive samples, and application in cohort-based joint calling. ResultsBy integrating k-mer-based and mapping-based methods, PanVariants significantly reduced variant errors (FPs + FNs), achieving a 73% reduction compared to BWA+GATK and a 45% reduction compared to DRAGEN for SNVs. Retraining the DeepVariant model with high-quality DNBSEQ data further decreased errors by 15%. For SVs detection, PanVariants attained an F1-score of 89.39%, markedly outperforming DRAGEN (68.18%) and BWA+Manta (58.33%), approaching long-read sequencing performance (95.22%). In validation using clinical positive samples, PanVariants successfully detected all expected pathogenic variants while PanGenie failed. In the cohort joint-calling analysis, PanVariants detected more variants, made fewer Mendelian inheritance errors, and gave better per-sample accuracy than GATK. ConclusionsPanVariants establishes a robust framework and best-practice pipeline for pangenome-based variant detection, achieving both sensitive novel variant discovery and high accuracy for SNVs, indels and SVs. Our systematic evaluation of optional processing steps and input variables offers practical guidance for users. Validated across diagnostic and population-based applications, our findings strongly support the transition from linear to pangenome references in future genomics.

bioinformatics↗

bioRxiv2026

Dual Pathways of Extracellular ATP Action in Cancer Cells: Purinergic Signaling Driven Senescence and Macropinocytic ATP Internalization

BackgroundOpportunistic nutrient uptake is a hallmark of cancer metabolism. Cancer cells upregulate macropinocytosis to acquire extracellular nutrients to support growth and stress adaptation. We previously showed that extracellular ATP (eATP) is internalized by macropinocytosis and promotes multiple cancer phenotypes. Here, we tested whether eATP uptake is prevalent across cancers and whether eATP also induces senescence through purinergic receptor (PR) signaling. MethodsIntracellular ATP (iATP) levels were measured following eATP exposure across multiple cancer cell lines. eATP internalization was visualized in vitro and in vivo using a non-hydrolyzable fluorescent ATP analog together with high-molecular-weight dextran as a macropinocytosis marker. Senescence was quantified using three SA-{beta}-galactosidase assays and flow cytometry. Pharmacologic inhibitors of macropinocytosis and purinergic receptors were used to define pathway dependence. Combination treatments with the glucose transporter inhibitor DRB18 and the senolytic navitoclax were evaluated for antiproliferative effects. ResultseATP produced dose- and time-dependent increases in iATP across diverse cancer cell types. Imaging demonstrated widespread macropinocytic internalization of ATP in vitro and in tumor xenografts. eATP induced senescence in NSCLC cells, confirmed by multiple {beta}-gal assays and flow cytometry. PR inhibition significantly reduced senescence, whereas macropinocytosis inhibition had minimal effect on senescence induction. ConclusionseATP acts through dual pathways in cancer cells: macropinocytic internalization that elevates iATP and PR signaling that drives senescence. Targeting metabolic uptake together with senolytic therapy may offer a novel anticancer strategy.

cancer biology↗

bioRxiv2026

Cardiac oxidative stress monitoring enabled by hierarchical mechanical adaptation

Soft bioelectronics have advanced cardiac monitoring through electrophysiological tracking, yet this alone cannot resolve the metabolic pathology essential to surgical decision-making. However, real-time molecular sensing on beating hearts remains unresolved due to deformation-induced sensor failure and stress-induced metabolite artifacts. This challenge is exemplified by ischemia-reperfusion injury (IRI), a major cardiac surgery complication characterized by reactive oxidative species (ROS) bursts, where true pathological ROS signals being confounded by mechanotransduction-induced ROS artifacts. Herein, we propose an enzymatic cardiac oxidative stress biosensor (E-cardiac) with hierarchical mechanical adaptation: macro-scale biofluid-mediated contact, micro-scale fiber reorganization, and nano-scale enzymatic confinement within gold nanoarches dissipate interfacial stress. This produces ultrathin ([~]460 nm), soft (0.79 kPa) E-cardiac with robust electrochemical stability (100% strain), low detection limit (380 nM), rapid adhesion (<3 s), stable biosensing on beating heart, as well as minimal invasive deployment capability. Mechanical analysis and cellular studies confirm mitigated stress-induced ROS and absent PIEZO channel activation. Validated across cardiomyocytes, ex vivo tissues, multi-species ischemia models (mouse, rat, rabbit, pig), rat ischemia-reperfusion injury, and Langendorff hearts simulating graded perfusion deficits, E-cardiac quantitatively differentiates IRI severity (sham < ischemia < reperfusion) as well as detecting the "ECG blind window". The E-cardiac platform provides real-time metabolic feedback for surgical guidance during cardiac procedures, enabling timely intervention before irreversible damage.

bioengineering↗

bioRxiv2026

Integrated bioinformatics and single-cell analysis identifies vascular aging-related hub genes and immune drivers in atherosclerosis.

Atherosclerosis (AS) is a chronic inflammatory disease closely linked to vascular senescence, yet the specific molecular mechanisms connecting aging processes to AS pathogenesis remain incompletely understood. This study integrated transcriptomic data from GEO datasets (GSE100927 and GSE43292) to identify vascular aging-related differentially expressed genes (VARDEGs). Following batch effect correction, 28 VARDEGs were screened and subjected to functional enrichment, protein-protein interaction (PPI) network analysis, and immune infiltration assessment. Seven hub genes (MMP9, APOE, TNF, ICAM1, PPARG, CYBA, and NCF2) were identified and experimentally validated via qRT-PCR, confirming their significant upregulation in AS samples. Receiver operating characteristic (ROC) analysis demonstrated high diagnostic accuracy for six of these genes (AUC > 0.7), with TNF exhibiting superior performance. Immune infiltration analysis revealed profound alterations in 28 immune cell types, particularly monocytes and T cells, which correlated strongly with hub gene expression. Furthermore, single-cell RNA sequencing analysis (GSE184073) localized the expression of core genes predominantly to monocytes and T cells, highlighting TNF overexpression in T cells as a potential critical driver. Finally, molecular docking simulations suggested that curcumin exhibits strong binding affinity to these hub genes, particularly PPARG, providing a mechanistic basis for its therapeutic potential. Collectively, this study elucidates the landscape of vascular aging-related genes in AS, identifies novel diagnostic biomarkers, and proposes potential therapeutic targets involving immune modulation and natural compounds.

biochemistry↗

bioRxiv2026

Genome sequencing and multi-stage, blood-feeding, and tissue-specific transcriptome atlas of the Rocky Mountain wood tick provide a critical resource for this vector

Dermacentor andersoni, the Rocky Mountain wood tick, is an important vector for pathogens impacting human and animal health, including bovine anaplasmosis, Colorado tick fever, and Rocky Mountain spotted fever. A better understanding of the biology of this tick is needed for developing disease prevention and vector control strategies. A reference genome was assembled for D. andersoni using high-fidelity (HiFi) long-read PacBio sequences and Hi-C contact mapping, yielding a contiguous assembly in which most contigs matched one of 11 chromosomes. Genome annotation by the NCBI eukaryotic genome annotation pipeline revealed high gene content completeness, yielding a genome completeness score of 94.0% using the Arachnida ortholog dataset. Following genome sequencing, we identified specific genes involved in blood feeding across a range of tissue types and life stages for D. andersoni. To accomplish this, RNA-seq analysis was used to investigate differential gene expression across most organs in adult, nymphal, and larval D. andersoni before and after feeding. Based on this analysis, we identified several gene groups that are involved in blood feeding. Furthermore, we establish sex- and developmental-stage-specific transcriptional profiles. Collectively, this study advances knowledge of D. andersoni biology and enables the development of strategies to limit the spread of diseases transmitted by this tick.

genomics↗

bioRxiv2026

Rewiring the Human Brain: On the Fabric of Associative Thinking

Concept cells are neurons in the medial temporal lobe that represent an abstract concept, such as a familiar person, in a context-independent way. They are activated by heterogeneous and potentially multi-modal sensory input related to the concept, such as viewing a photo of the person, reading the persons name, or hearing the persons voice. Learning the concept implies connecting the cortical cells that are triggered when such features are perceived with the cells of the concept, resulting in an associative memory engram. Traditional models explain the formation of such an engram with Hebbian learning through synaptic plasticity, the strengthening of existing synapses in response to co-stimulation. However, the low edge density of the brain suggests that direct connections in the form of preexisting synapses between these cells are relatively unlikely, rendering such constructs inefficient and volatile. Instead, it is plausible that more persistent concept engrams rely on structural plasticity, involving the creation of synapses de novo. Yet, it has still been unclear how neurons can project their axons across such a considerable distance, finding a target they do not know in advance. In this paper, we simulate the formation of such structural engrams in the connectomes of healthy subjects, offering a model hypothesis of how such engrams can be formed on a structural level. Based on our model, we further demonstrate how activating a concept can trigger related concepts through overlapping sensory associations, in a process we call a percept-concept loop.

neuroscience↗

bioRxiv2026

Loss of Propionyl-CoA Carboxylase Reprograms Hepatic Metabolism by Suppressing Mitochondrial Pyruvate Carboxylation and Fatty Acid Oxidation

Propionic acidemia (PA) is an inborn error of metabolism caused by propionyl-CoA carboxylase (PCC) deficiency due to mutations in either PCCA or PCCB. Without proper management, the disease is associated with high mortality. Even with dietary restriction, patients often develop complications later in life, and the underlying pathological mechanisms remain poorly understood. The liver is the primary organ responsible for propionyl-CoA metabolism, yet the metabolic alterations induced by PCC deficiency in the liver have not been systematically investigated. In this study, we used a hepatocyte model of PA-- PCCAnull-HepG2 cells--to comprehensively examine metabolic alterations using stable isotope-based metabolic flux analysis. The PCCA knockout recapitulated key metabolic features of PA in HepG2 cells. Furthermore, PCCA deficiency reduced mitochondrial fatty acid oxidation while increasing glucose oxidation through pyruvate dehydrogenase. In contrast, pyruvate anaplerosis via pyruvate carboxylase was markedly reduced in PCCA knockout cells. This reduction in anaplerotic flux impaired the capacity for gluconeogenesis and lipid synthesis, consistent with observations from in vivo studies in Pcca-/- (A138T) mice. Additionally, branched-chain keto acid catabolism was reduced in PCCA knockout HepG2 cells. Threonine showed minimal metabolic contribution in this model, further supporting the role of propionate as a major source of propionyl-CoA production. Collectively, these findings highlight the metabolic vulnerabilities associated with PCC deficiency and underscore the increased risk of prolonged fasting in patients with PA, particularly those with severe disease.

genetics↗

bioRxiv2026

Resolution of the D4Z4 repeat responsible for facioscapulohumeral muscular dystrophy with HiFi sequencing

The D4Z4 macrosatellite repeat encompasses some of the most difficult-to-resolve disease-related variations in the human genome. D4Z4 has a repeat unit of 3.3 kb (encoding the DUX4 gene) that is present in up to 100 copies on two chromosomes (4 and 10), while DUX4 can only be expressed in somatic cells from the permissive A haplotype that usually occurs on chromosome 4. Facioscapulohumeral muscular dystrophy (FSHD) is caused by chromatin relaxation and ectopic expression of DUX4 in skeletal muscle, mediated by contraction of D4Z4 to 1-10 copies (FSHD1, 95% of FSHD cases) or mutations in chromatin factor genes such as SMCHD1 (FSHD2, 5% of FSHD cases). Due to its large size, disease specific haplotypes and sequence homology between chromosomes, D4Z4 is challenging to resolve by current sequencing technologies. We report a computational tool, Kivvi, to genotype D4Z4 using PacBio whole-genome long-read sequence data. Kivvi detects all D4Z4 alleles in a sample, reporting the repeat size, chromosome (4 vs. 10), distal haplotype (A vs. non-permissive haplotypes) and the methylation level of each allele. We validated Kivvi against gold standard assays for FSHD diagnostics, detecting 100% of contracted alleles and correctly classifying 90% of noncontracted alleles. We showed differential methylation signals between FSHD1 and candidate FSHD2 samples. We profiled D4Z4 across 601 individuals from five ancestral populations, revealing extensive genetic diversity. We identified common haplotypes of D4Z4 alleles and characterized hybrid repeat units, hybrid repeat arrays, and translocation alleles. Combined with HiFi long reads, Kivvi enables the consolidation of multiple FSHD assays into a single workflow and facilitates the discovery of novel genetic modifiers of FSHD through population-scale studies.

genetics↗

bioRxiv2026

Path Integration and Spatial Updating Recruit Distinct Cognitive-Neural Mechanisms in Humans

Path integration and spatial updating refer to the integration of self-motion information during navigation to update ones start location and the positions of other locations, respectively. Even though path integration has been described as a fundamental process whose output may serve as a building block for other navigational computations like spatial updating, the exact relationship between path integration and spatial updating is unknown. Here we addressed this question with an eye-tracking behavioral experiment and a subsequent fMRI study. Despite experiencing identical self-motion cues, participants showed differential eye fixation patterns and responded more quickly during spatial updating than during path integration, casting doubt on the fundamental role of path integration. Neuroimaging results showed that the precuneus and the dorsal premotor cortex were more activated during spatial updating, but the precuneus had stronger functional connectivity with the thalamus and the frontal cortex during path integration. Further supporting this dissociation, the two tasks invoked distinct brain-wide inter-regional functional networks. Together, the combined findings of both experiments suggest that spatial updating and path integration are dissociable navigation processes supported by distinct behavioral and neural mechanisms, rather than one process operating on the basis of the other.

neuroscience↗

bioRxiv2026

Parkinson's disease-linked D620N mutation selectively alters the brain-specific protein interactome of VPS35

Mutations in several genes are known to cause familial forms of Parkinsons disease (PD), including mutations in the vacuolar protein sorting 35 ortholog (VPS35) gene linked to late-onset, autosomal dominant PD. VPS35 encodes a core subunit of the retromer complex which functions in endosomal sorting and recycling. It remains unclear how the pathogenic D620N mutation in VPS35 disrupts retromer function to induce neurodegeneration in PD. Using cell-and rodent-based models expressing D620N VPS35, we performed interactome proteomics to identify alterations underlying the pathogenic effects of D620N VPS35 in PD. Using overexpression of VPS35 variants in HEK-293T cells, we conducted tandem affinity purification (TAP) or co-immunoprecipitation (co-IP) with protein chemical crosslinking to determine the native and non-native protein interactomes of wild-type (WT) and D620N VPS35, respectively. Notably, we can confirm the reduced interaction of D620N VPS35 with components of the WASH complex. Additionally, using a viral-mediated gene transfer model of human D620N VPS35 overexpression in adult rat brain, we identify the first brain-specific protein interactome of VPS35. These overexpression models reveal remarkably similar interaction profiles of WT and D620N VPS35, suggesting that the D620N mutation has a subtle effect on the overall VPS35 protein interactome. We also conducted proteomic analysis of brain tissue from a D620N VPS35 knockin (KI) mouse model that expresses VPS35 at endogenous levels. Using co-IP from hemi-brain or striatal extracts of WT and D620N VPS35 KI mice, we reveal a high degree of similarity between the brain interactomes of WT and D620N VPS35, further suggesting a subtle effect of the D620N mutation on VPS35 protein interactions. Notably, in both hemi-brain and striatum, we find a selective decrease in the interaction of two known interactors, TBC1D5 and VPS29, with D620N VPS35. We also performed global proteomic analysis of striatal tissue from D620N VPS35 KI mice and reveal a high degree of similarity between WT and D620N, further suggesting a subtle effect of this mutation. Together, our study provides a comprehensive evaluation of the VPS35 protein interactome and reveals a selective effect of the PD-linked D620N mutation in mammalian cells and brain. Our study provides key insight into the mechanisms of retromer dysfunction in VPS35-linked PD.

neuroscience↗

bioRxiv2026

Natural variation in DXR expression is associated with apical hook bending under NaCl stress in Arabidopsis thaliana

Successful soil emergence requires apical hook establishment during skotomorphogenesis. Soil salinity disrupts this process, but the mechanisms linking environmental stress to hook growth remain unclear. Here, we employed a genome-wide association study (GWAS) across Arabidopsis thaliana accessions to identify a locus associated with variation in the salt-induced reduction of apical hook curvature. Fine mapping reveals genetic variation in the promoter of 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE (DXR), encoding the first committed enzyme of the plastid-localized methylerythritol phosphate (MEP) pathway. Accessions carrying an alternative promoter haplotype exhibit elevated DXR expression and a stronger hook bending under salt. Salt treatment and loss of transcriptional repressor PHYTOCHROME INTERACTING FACTOR1 (PIF1) additively increase DXR transcript levels, and pif1-2 seedlings exhibit higher apical hook angles under salt stress. This phenotype is suppressed by inhibition of DXR activity, indicating that an increased MEP pathway flux reduces salt sensitivity in pif1-2 seedlings. Across accessions, DXR expression positively correlates with hook curvature under salt stress, further strengthening the link between DXR and modulation of hook bending under salt stress. Together, these findings identify plastid metabolism as a regulatory layer linking environmental stress to altered skotmomorphogenis, and raise important questions about how etioplast-derived signals interact with growth-control networks in the dark. HighlightA genome wide association study in Arabidopsis reveals that variation in DXR expression, encoding an essential enzyme in the MEP pathway, drives salt-induced repression of apical hook formation darkness.

plant biology↗

bioRxiv2026

Protenix-v2: Broadening the Reach of Structure Prediction and Biomolecular Design

Advances in biomolecular modeling have broadened the range of problems addressable by structure prediction and design models. Here, we present results from Protenix-v2, a system spanning high-accuracy structure prediction and biomolecular design. On the structure prediction side, Protenix-v2 achieves antibody-antigen success rates with up to 13-point gains over Protenix-v1, while 5-seed performance surpasses previous 1000-seed results. On the design side, Protenix-v2 demonstrates a 100% target-level success rate in novelty-controlled VHH-Fc campaigns, reaching hit rates up to 48%. Crucially, the model enables hit discovery on difficult GPCR targets with hit rates of 16%-88% (VHH-Fc) and up to 50% (mAb) under 16-30 testing budgets per target. Resulting hits show high developability and diversity. Beyond antibody tasks, we report improved ligand-related plausibility and successful cross-variant SARS-CoV-2 spike RBD mini-binder design. These results establish Protenix-v2 as a robust and powerful model for accelerated drug discovery.

molecular biology↗

bioRxiv2026

Topographic structure and function of locus coeruleus norepinephrine neurons

Norepinephrine (NE) is released throughout most of the central nervous system by neurons in the locus coeruleus (LC). We found a relationship between the morphologies, gene expression, and activity of LC-NE neurons in mice. Axonal projections of individual neurons were extensive but largely confined to subsets of brain regions. Axonal projections and graded gene expression correlated with locations of cell bodies in LC. In a behavioral task requiring ongoing learning from actions, neurons in dorsal LC projecting to the cerebral cortex were excited when mice made a different choice from the previous one and by reward prediction errors, a signal driving learning. Background activity of neurons in ventral LC was higher when mice ignored stimuli indicating potential reward availability. These observations reveal a topographically organized structure and function of a neurotransmitter system and show that it contains learning signals for flexible behavior.

neuroscience↗

bioRxiv2026

RUNX1-deficiency drives immune-active ER+ mammary tumorigenesis through activation of interferon signaling

AbstractRecurrent loss-of-function mutations in RUNX1 occur in estrogen receptor-positive (ER+) breast cancers, yet how RUNX1-loss contributes to breast tumorigenesis remains unclear. Here we used genetically engineered mouse models with luminal mammary epithelial cell (MEC)-restricted gene disruption to investigate its role in breast cancer initiation. Loss of RUNX1 alone, or together with RB1, was insufficient to drive tumor formation. In contrast, combined loss of RUNX1 and p53 induced mammary tumors with full penetrance. These tumors contained ER+ cancer cells and exhibited extensive T cell and macrophage infiltration, indicative of an immune hot microenvironment. Mechanistically, RUNX1-deficiency activated interferon signaling in luminal MECs, associated with derepression of RUNX1 target STAT1 and enhanced inflammatory responses. Consistent with these findings, human ER+ breast cancers with low RUNX1 expression displayed elevated immune signatures and poorer patient survival. Together, our results identify RUNX1-loss as a driver of an immune-active subtype of ER+ breast cancer.

cancer biology↗

bioRxiv2026

Cryo-EM elucidation of stoichiometric plasticity, asymmetric ligand recognition and allosteric coupling in human P2X2/3 heterotrimeric channels

P2X receptors are trimeric ATP-gated ion channels that assemble as homo- or heterotrimers, with heteromeric forms exhibiting intrinsic asymmetry that influences function. Here, we report four high-resolution cryo-EM structures of human P2X2/3 heterotrimers representing distinct functional states, including ATP-bound assemblies (P2X332 and P2X223), the apo form, and a ligand/ATP-bound closed conformation. The three ATP-binding sites show asymmetric recognition of MgATP{superscript 2}- and ATP-, and channel activation requires occupancy of only two MgATP{superscript 2}- molecules. Gefapixant binds a single allosteric site and selectively inhibits MgATP{superscript 2}-, but not ATP-, binding, indicating orthosteric-allosteric coupling within the heterotrimer. Structural features of the transmembrane domain define ion permeation, particularly for Ca{superscript 2}. Despite asymmetric ligand interactions, gating remains largely symmetric, with minor differences in desensitization. These findings provide a structural framework linking asymmetry to coordinated channel function and open avenues for subtype-selective therapeutic intervention.

biophysics↗