Biology subjects

Xie, C.

Publications and source records attributed to Xie, C..

At least 19 recordsLinked to original sources

bioRxiv2026

The Arabidopsis PAL3 is a carboxy-tyrosine ammonia lyase

Phenylalanine ammonia lyase (PAL) catalyses the deamination of L-phenylalanine, which is the first step of the plant-specific phenylpropanoid pathway. Its position at the intersection of primary and specialized metabolism, combined with its important role in plant growth and adaptive stress response, has made it a subject of extensive studies. We identified key amino acids in the catalytic pocket of several PAL enzymes, including PAL3 of Arabidopsis, that are different from the canonical PAL sites, suggesting these enzymes have a different substrate specificity and have been miscategorised for decades. By combining untargeted metabolomics with enzyme assays, we discovered that PAL3 converts 3-carboxy-tyrosine into carboxy-p-coumaric acid. Based on this specific function, we propose to denote it as a 3-carboxy-tyrosine ammonia lyase (CAL). In addition to its discovery as a novel enzyme class, paving the way for biotechnological applications, we introduce the carboxy-phenylpropanoids as a new class of specialised metabolites.

biochemistry↗

bioRxiv2026

De novo design of CR2 binder as vaccine scaffold

Efficient B cell activation during vaccine-induced humoral immunity relies on both B cell receptor (BCR) antigen recognition and synergistic signaling from co-receptors. Complement receptor 2 (CR2), the primary BCR co-receptor on B cells, lowers the activation threshold and amplifies downstream kinase signaling by orders of magnitude when engaged by complement fragment C3d decorated antigens. Targeting CR2 therefore represents a rational vaccine enhancement strategy, yet native C3d suffers from low affinity, poor stability, and manufacturing challenges. Here, we report the de novo design of a highly stable, high-affinity CR2 binder using deep learning driving protein design methods. Biophysical characterization, high-resolution cryoEM structural determination, and functional assays in vitro and in vivo confirm that the designed binder matches computational design models and specifically engages CR2 to boost B cell activation. When fused to antigen as a vaccine scaffold, the trimeric CR2 binder elicits robust humoral immune responses comparable to nanoparticle vaccines, while retaining the simplicity of single-chain protein production. Our work establishes a modular CR2 targeting vaccine scaffold platform with broad translational potential for next-generation protein vaccines.

immunology↗

bioRxiv2026

Djp1 is a multifunctional Hsp40 cochaperone for mitochondrial phospholipid metabolism

Mitochondria are cellular energy hubs best known for ATP production via oxidative phosphorylation; however, they also serve as biosynthetic centers for phospholipids. Mitochondrial phospholipids are critical for various cellular processes, and their loss underlies myriad mitochondrial diseases. The critical enzymes underlying these biosynthetic cascades are encoded in the nucleus, translated in the cytosol, and imported into mitochondria. Understanding of mechanisms and factors that ensure precise targeting of proteins to mitochondria has been long overlooked but remains critical. Recently, the J-protein/Hsp40 cochaperone Djp1 has emerged as a key player in mitochondrial protein targeting by promoting the transfer of precursors from the endoplasmic reticulum (ER) surface to mitochondria in a pathway termed ER-SURF. Molecular details regarding how Djp1 recognizes clients and more broadly supports mitochondrial function remain unknown. Using biochemical approaches, proteomics, and thin layer chromatography, we demonstrate that Djp1 is a regulator of Phosphatidylserine decarboxylase 1 (Psd1), an inner mitochondrial membrane resident responsible for mitochondrial phosphatidylethanolamine (PE) production. This regulation of Psd1 biogenesis is dependent on its mitochondrial targeting signal and is specific to Djp1 compared to other members of the Hsp40 family or ER targeting factors. Intriguingly, the combined loss of Djp1 and Psd1 results in a synthetic sick phenotype that unexpectedly reflects a role(s) for Djp1 in proper mitochondrial phospholipid metabolism independent of Psd1. Taken together, these findings expand our understanding of Djp1-dependent mitochondrial protein regulation and unveil Djp1 as important for mitochondrial phospholipid metabolism by multiple mechanisms.

cell biology↗

bioRxiv2026

IKKβ as a putative non-covalent and quinone-mediated covalent target of 4-methylcatechol in RANKL/NF-κB signaling: a combined computational and experimental analysis

Excessive osteoclast activity contributes to pathological bone loss in osteoporosis, rheumatoid arthritis, and osteolytic malignancies. The effects of small catechol derivatives on receptor activator of nuclear factor-{kappa}B ligand (RANKL)-induced osteoclastogenesis remain poorly understood. This study investigated the effects of 4-methylcatechol (4-MC) on RANKL-induced NF-{kappa}B activation and osteoclast differentiation. 4-MC reduced RANKL-induced NF-{kappa}B luciferase activity in HEK-293T/RANK cells. 4-MC also suppressed RANKL-induced TRAP activity in RAW264.7 cells in a concentration-dependent manner and reduced the number of TRAP-positive multinucleated osteoclasts, without affecting cell viability. Molecular docking predicted non-covalent binding of 4-MC within the ATP-binding hinge region of IKK{beta} (PDB: 4KIK), forming a close polar contact with Glu97, predicted hydrogen bonds with Cys99, and a hydrophobic contact with Ile165, within the pocket occupied by the co-crystallized inhibitor K252a. Covalent docking predicted that the oxidized quinone form of 4-MC engages Cys179 in the IKK{beta} activation loop. Quantum chemical calculations confirmed a markedly higher electrophilicity index for the oxidized quinone than for the parent catechol, supporting this mechanism. In silico ADMET profiling indicated favorable drug-likeness and safety. These findings identify IKK{beta} as a plausible molecular target of 4-MC through both non-covalent and covalent mechanisms. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/741661v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1d9f82eorg.highwire.dtl.DTLVardef@134a24borg.highwire.dtl.DTLVardef@8aeb91org.highwire.dtl.DTLVardef@6fb85d_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

Cerebrovascular Imaging-to-Graph Reconstruction for Individualized Digital Twin Brains

The development of digital twins in medicine, i.e., virtual replicas of human organs, offers a promising path toward precision medicine by enabling interpretable, mechanistic, and actionable insights. In the brain, cerebrovascular twins support individualized modeling of hemodynamics and bio-transport, with broad applications. A major bottleneck, however, is the lack of robust methods to transform in vivo cerebrovascular images into simulation-ready cerebrovascular meshes or graphs. Here, we present CerebroVascular Imaging to Graph reconstruction (CVIG), a robust and multiscale framework for reconstructing whole brain cerebrovascular graphs from in vivo cerebrovascular images. CVIG integrates vessel vectorization, with tolerance to discontinuity in vessel structures, using a topology-guided assembly of vessel trees to generate cerebrovascular graphs from medical images. We demonstrate the ability of CVIG to generate vascular graphs with improved vascular coverage and topological correctness, the capability essential for high fidelity brain biophysical simulations. This work establishes a vascular graph framework for individualized modeling and analysis, providing a key foundation for digital twins of the human brain.

bioengineering↗

bioRxiv2026

Learning induces activation-mechanism--dependent neural plasticity in an intracortical microstimulation task

Electrical microstimulation provides high-resolution control of neural circuits for causal studies and restoration of impaired functions, yet how responses to artificial activation evolve with learning remains unclear. Here, we deploy a detection task and pair ultraflexible electrodes for stable intracortical microstimulation (ICMS) with longitudinal imaging and recordings to track single-cell and population responses across weeks of learning. Detection thresholds decreased with learning, indicating plasticity. Chronic imaging showed that stimulus-evoked recruitment expanded at a fixed current, while a consistent number of neurons continued to underlie behavioral responses. A subset of learning-sensitive cells enhanced modulation and reduced latency. Electrophysiological recordings further distinguished two forms of adaptation: directly activated, pulse-locked neurons strengthened their excitability, whereas polysynaptically recruited neurons expanded in number and were predictive of behavioral outcomes. These results show that learning in an ICMS task reshapes cortical circuits through activation-mechanism-dependent plasticity, underscoring the need for stimulation paradigms that adapt to both cell-intrinsic and network dynamics. One-sentence summaryLearning alters neural responses to ICMS, revealing differences between direct activation and network activity linked to behavior.

neuroscience↗

bioRxiv2026

Prediction of Transcription Factor DNA Binding Affinity with High-Throughput Kd Measurements and Deep Learning

Transcription factors (TFs) regulate gene expression through specific interactions with genomic DNA. While TF binding motifs from public databases describe sequence preferences, quantifying genome-wide affinity (Kd) is highly desirable for a more accurate thermodynamic description. Here, we report ivtFOODIE (in vitro FOOtprinting with DeamInasE), an assay that leverages deaminase-mediated cytosine-to-uracil conversion to measure Kd values for a given TF across accessible genomic regions from human cells. By pre-training on TF binding sites from JASPAR and fine-tuning with our ivtFOODIE data from 46 TFs representing 13 different DNA-binding domains (DBDs), we developed Seq2Kd, a deep learning model capable of predicting a TFs absolute binding affinity on DNA sequences. Seq2Kd enables de novo motif discovery of [~]500 previously uncharacterized human TFs and reveals the effects of genetic variation both in TF-coding regions and DNA-binding sites on gene expression and disease susceptibility. By correlating predicted affinity changes with the sign and magnitude of expression quantitative trait locus (eQTL) effects, we stratified TFs into activator-like and repressor-like groups. Compared to clinically benign variants, pathogenic single-nucleotide variants (SNVs) within regulatory and protein-coding regions show significantly larger predicted shifts in Kd. We provide an interactive web portal, the ENcyclopedia of Transcription-factor Interactions with Regulatory Elements (ENTIRE), which integrates the Seq2Kd model with the ivtFOODIE dataset. This resource offers thermodynamic prediction for TF-DNA interactions for functional genomics and human disease.

biophysics↗

bioRxiv2026

De novo steroidogenesis maintains female-specific Th2 identity and constrains effector function

T helper 2 (Th2) lymphocytes drive type-2 immunity and allergic diseases that disproportionately affect females, yet the mechanisms underlying this sexual dimorphism remain poorly understood. Current models attribute sex-biased immune differences to circulating gonadal hormones and to sex chromosome composition, leaving unresolved whether immune cells possess cell-autonomous mechanisms acting independently of both. Here we show that female and male Th2 cells differentiated under identical, hormone-free conditions are transcriptionally distinct but functionally equivalent: female cells carry a heightened inflammatory and interferon-response programme, yet produce IL-13 and IL-4 at rates indistinguishable from male cells, with only a modest baseline difference in proliferative capacity. Using T cell-specific deletion of Cyp11a1 that encodes the first and rate-limiting enzyme of de novo steroidogenesis, we identify the constraint that maintains this equivalence. Cyp11a1 loss acts almost exclusively in females, where it simultaneously dampens the female-specific inflammatory programme and drives proliferation and IL-13 production above the level seen in either sex. Male Th2 cells are essentially unaffected. The effect requires differentiation, being absent in naive precursors, indicating that the steroidogenic machinery becomes functionally consequential only in the mature effector state. Cross-species analysis of two human atopic dermatitis single-cell datasets identifies a shared directional signature of gene expression. Cell-intrinsic steroidogenesis therefore constitutes a third axis of immunological sexual dimorphism, one that operates by uncoupling transcriptional identity from effector output rather than by specifying identity itself.

immunology↗

bioRxiv2026

Rewiring Mitochondrial Phosphatidylethanolamine Metabolism Identifies New and Unaccounted Trafficking Steps

The distinct compositions of the two mitochondrial membranes are generated through a combination of phospholipids that mitochondria can make and those they take; both processes depend on a series of distinct lipid trafficking steps. Mitochondria make phosphatidylethanolamine (PE) through the action of the phosphatidylserine decarboxylase Psd1, an intermembrane space (IMS)-facing integral inner membrane (IM) protein. Psd1 has been proposed to act on its endoplasmic reticulum-derived substrate, phosphatidylserine (PS), after its transport to the mitochondrial outer membrane (OM) and either following its Ups2/Mdm35-mediated transport across the IMS to the IM or instead, on the IMS-side of the OM in a process enabled by the mitochondrial contact site and cristae organizing system (MICOS). Here, we implement a two-pronged Psd1 rewiring-based strategy predicted to either 1) circumvent the need for Ups2/Mdm35 and/or MICOS; or 2) selectively ablate the ability of Psd1 to work in trans. Our results with yeast harboring Psd1 targeted to the OM demonstrate that, with respect to mitochondrial PE production, Ups2/Mdm35 and MICOS indeed function within the IMS. Using yeast expressing a topologically inverted Psd1 chimera that faces the matrix, we identify previously unappreciated transbilayer lipid trafficking steps within the IM and show that Psd1 does not operate via a MICOS-organized in trans mechanism. Further, retained flux through inverted Psd1 when both Ups2/Mdm35 and MICOS are absent strongly implicates the existence of a major, yet presently unknown, mediator(s) of lipid movement across the IMS. Collectively, these data suggest a new model of how mitochondrial membrane diversity is established and maintained.

cell biology↗

bioRxiv2026

High-channel-count neural recording and stimulation platform with 5,376 simultaneous recording channels

Advancing neural interfaces requires large-scale, high-density recording technologies capable of capturing full-spectrum neural activity across cortical and subcortical regions. Here, we present a scalable approach to integrate neural electrodes with advanced application-specific integrated circuits (ASICs). Specifically, we custom-designed an ASIC with 5,376 simultaneous channels, each sampling at 20 kS/s and enabling >1.3 Gb/s total data streaming throughput. The ASIC incorporates in-pixel amplification, time-division multiplexed ADCs, and on-chip stimulation capabilities, ensuring precise signal acquisition with minimal power consumption while maintaining a low noise level of 5.5 {micro}Vrms. We further developed an interconnect strategy using gold bump bonding, which allows for high-density integration of the flexible probe and rigid chip. We demonstrate the capacity of this platform through the integration with a flexible ECoG array. The resulting device allows for the high-resolution mapping of in vivo field potentials on the cortical surfaces of rat brains, supported by the precise localization of evoked sensory activities. These results prove an effective approach towards highly integrated neural interfaces with applications in brain-computer interfaces, neuroprosthetics, and large-scale functional brain mapping.

bioengineering↗

bioRxiv2026

Digital Twin Brain simulation and manipulation of a functional brain network underlying mental illness

Linking synaptic-level perturbations to distributed brain-network dynamics remains a central challenge for understanding and treating mental illness. Although recent whole-brain models can reproduce individual brain activity patterns, they largely function as descriptive simulators rather than mechanistic, intervention-capable systems. Here we present an intervention-capable digital twin of the human brain, integrating individual neuroanatomy and task-evoked dynamics within a neuronal-scale framework. Individualised digital twin brains recapitulate a participant-specific compact cortico-subcortical network phenotype that captures transdiagnostic psychopathology across population and clinical cohorts. In silico modulation of excitatory and inhibitory synaptic conductance produces bidirectional, heterogeneous network responses across individuals. Population-scale simulations stratify individuals and predict longitudinal symptom trajectories from DTB-derived response profiles. Independent pharmacological functional MRI data further validate the predicted baseline-dependent network responses in vivo. Together, these findings establish digital brain models as experimental platforms for mechanistic perturbation, behavioural prediction and stratification, providing a foundation for precision neuroscience and psychiatry.

neuroscience↗

bioRxiv2026

Genome-wide maps of transcription factor footprints identify noncoding variants rewiring gene regulatory networks with varTFBridge

Genome-wide association studies have identified millions of noncoding loci linked to human traits, yet how these variants alter gene regulation remains a major challenge, particularly for rare variants where whole-genome sequencing cohorts and high-resolution functional annotations remain limited. Here we show that single-molecule deaminase footprinting (FOODIE) in K562 cells captures up to 103-fold heritability enrichment for erythroid traits despite covering 0.12% of the genome. We introduce varTFBridge, integrating FOODIE footprinting with AlphaGenome variant effect prediction to identify causal noncoding variants altering transcription factor (TF)-mediated regulation. Applied to 490,640 UK Biobank genomes across 13 erythrocyte traits, varTFBridge prioritises 113 high-confidence regulatory variants (104 common, 9 rare), encompassing 2,173 linkages along the variant-TF binding- gene-trait cascade across 64 TFs and 108 genes. varTFBridge recapitulates rs112233623 and resolves its mechanism: GATA1/TAL1 co-binding disruption at a CCND3 enhancer altering red blood cell count and volume.

bioinformatics↗

bioRxiv2026

Asarinin Inhibits RANKL-Induced Osteoclast Differentiation by Targeting the p38/ERK-c-Fos-NFATc1 Axis

Excessive osteoclast formation is a key contributor to pathological bone loss in disorders such as osteoporosis and rheumatoid arthritis. Asarinin, a natural lignan, has not previously been examined in the context of osteoclast differentiation. Here, we investigated the anti-osteoclastogenic effects of asarinin using RANKL-stimulated RAW264.7 cells. Asarinin significantly suppressed TRAP-positive multinucleated osteoclast formation under the tested conditions. Mechanistically, asarinin selectively inhibited RANKL-induced phosphorylation of p38 and ERK MAPKs, leading to reduced c-Fos expression and inhibition of NFATc1 nuclear translocation. In addition, asarinin disrupted actin ring formation in mature osteoclasts. Collectively, these findings identify asarinin as a pathway-selective inhibitor of osteoclast differentiation, targeting the p38/ERK-c-Fos-NFATc1 axis while sparing parallel signaling pathways.

pharmacology and toxicology↗

bioRxiv2026

Methyl Carnosate, a Carnosic Acid Derivative, Attenuates Osteoclastogenesis via Modulation of RANKL-Induced NF-κB Activity

Excessive osteoclast activity underlies bone-destructive diseases including osteoporosis and rheumatoid arthritis. RANKL-induced NF-{kappa}B signaling represents a critical pathway driving osteoclastogenesis. Here, we report that methyl carnosate, a naturally occurring diterpene from rosemary, inhibits RANKL-induced osteoclastogenesis with an IC50 of 1.2 M and displays greater potency than its parent compound, carnosic acid. Promoter-reporter analysis further indicates attenuation of RANKL-induced NF-{kappa}B activity. These findings identify methyl carnosate as a potential lead compound for the development of bone-protective therapeutics.

pharmacology and toxicology↗

bioRxiv2025

Closing the Sim-to-Real Gap: An End-to-End Robotic Ultrasound System Leveraging In Vivo Reinforcement Learning and 3D-Prior Guided Hybrid Control

Abdominal ultrasound is a crucial first-line diagnostic tool, yet its efficacy is inherently constrained by a strong dependency on operator skill, leading to significant inter-operator variability and limiting its widespread adoption. While robotic ultrasound systems with artificial intelligence have emerged to mitigate this, current approaches face critical limitations: they often rely on simulated or phantom data for training, which hampers generalizability, and employ control strategies that lack the flexibility to adapt to complex human anatomy. To address these challenges, this paper introduces a novel, end-to-end robotic system for autonomous abdominal scanning. Our methodology is systematic: it begins with coarse scan planning via RGB and 3D point cloud-based localization of key anatomical landmarks (e.g., xiphoid process). The core of our approach involves training a reinforcement learning scanning policy directly on live human volunteers, enabling the development of a strategy that is robust to anatomical diversity. This high-level policy is executed by a sophisticated hybrid force-position controller, enhanced with real-time normal vector calibration and 3D point cloud-based respiratory phase detection to dynamically adjust contact force, particularly during inspiration. This innovation proves critical for improving scan quality in subjects with higher Body Mass Index (BMI). Extensive validation against expert sonographers demonstrates that our system achieves high precision in standard plane recognition and superior scanning efficiency. Furthermore, to holistically assess performance where standard planes are difficult to acquire, we introduce a 3D reconstruction-based coverage metric. Results confirm that our system delivers strong adaptability and significantly improved consistency, marking a substantial step toward clinically viable, operator-independent ultrasound robotics.

bioengineering↗

bioRxiv2025

Metabolic engineering of a tyrosine-specific phenylpropanoid pathway in plants

While all plants use L-phenylalanine for phenylpropanoid biosynthesis, grasses can also initiate the pathway from L-tyrosine. Curiously, no plant has evolved an exclusive tyrosine-derived route. We generate plants with phenylpropanoid biosynthesis initiated from phenylalanine, tyrosine, or both by expressing a Brachypodium phenylalanine/tyrosine ammonia-lyase (PTAL) in Arabidopsis WT and c4h mutants. Engineering a bifunctional phenylpropanoid pathway in WT plants did not negatively impact growth, while introducing a tyrosine-specific pathway in the c4h mutant could overcome the seedling-lethal phenotype. Interestingly, restored c4h mutants relying solely on the tyrosine route displayed developmental defects linked to the strong overaccumulation of the auxin transport inhibitor cis-cinnamic acid. Our findings suggest that the requirement of this widely overlooked plant metabolite could be the crucial factor for the evolutionary retention of the canonical phenylpropanoid biosynthesis route via L-phenylalanine in plants.

plant biology↗

bioRxiv2025

Windows to the goal: Pupillary working memory signatures prospectively adapt to task demands

The pupillary light response was once considered a brainstem reflex, but newer findings indicate that pupil dilation can also reflect content held in mind with working memory (WM). This suggests that WM may recruit even the earliest sensorimotor apparatus for maintenance. Here, we tested two boundaries of this pupillary WM response: whether it generalizes beyond low-level stimuli and whether it adapts to changing behavioral goals. Namely, we tested whether the pupils reflect remembered brightness for real-world scene images, and whether the effect varies when different features dimensions are emphasized for the memory test (i.e., visual detail vs. semantic category). We found a feature-specific pupillary WM effect for remembering natural scenes, but only when the task encouraged a visual maintenance strategy. Rather than a retrospective echo of sensory-evoked stimulus features, the pupillary WM response prospectively adapts to how the memory content will be used.

neuroscience↗

bioRxiv2025

Hyperactivated Glycolysis Drives Spatially-Patterned Kupffer Cell Depletion in MASLD

Metabolic dysfunction-associated steatotic liver disease (MASLD) progression is characterized by hepatic inflammation and cell death, yet the mechanisms underlying Kupffer cells (KCs) loss remain poorly understood. Here, we sought to elucidate the metabolic basis of KCs death during MASLD. Using metabolomics, immunostaining, and flow cytometry, we evaluated metabolic alterations and KCs death throughout early MASLD progression. We found that KCs death is an early hallmark of MASLD, exhibiting greater susceptibility and displaying a spatial distribution consistent with KCs zonation. Moreoever, KCs undergo progressive metabolic reprogramming toward enhanced glucose utilization during MASLD development, which is correlated with KCs death. In combination of biochemical agonist, isotope tracing and primary KCs culture, we further demonstrated that augmented glycolytic metabolism directly drives KCs death in vitro. Consistently, using Chil1-deficient mice, we further demonstrated that increased glucose utilization accelerates KCs death in vivo. Together, these findings establish a causal link between glycolytic activation and KCs loss during MASLD progression, highlighting glucose metabolic pathways as potential therapeutic targets to preserve KCs homeostasis and mitigate MASLD.

pathology↗