Biology subjects

Zhang, H.

Publications and source records attributed to Zhang, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Live imaging reveals oocyte membrane pre-remodeling forming permissive space for asymmetric division

Abstract Successful oocyte maturation requires first polar body (PB1) extrusion, yet how the oocyte prepares for this asymmetric event remains unclear. Live membrane imaging of mouse oocytes reveals pronounced regional heterogeneity in plasma-membrane dynamics, generating an early polarized pattern across the surface. Whereas most of the oocyte surface and its microvilli remain relatively stable, a discrete membrane domain collapses and retracts around germinal vesicle breakdown (GVBD), separating from the zona pellucida to establish a pre-extrusion space (PES). Transient oocyte comb-like protrusions arise within the PES and subsequently collapse, converting the protrusion-filled region into an open cavity before PB1 extrusion. Mechanistically, early ERK28 dependent dissociation of the cortical scaffold ZO-1 is required for this space to form. ERK2 phosphorylates ZO-1, suppresses its phase separation, and promotes its removal from the cortex. Blocking MEK-ERK signaling prevents ZO-1 dissociation, abolishes pre-extrusion space formation, and impairs PB1 extrusion, whereas ERK activation restores these events in aged oocytes. Together, our findings identify a membrane collapse-based pre-remodeling mechanism that licenses PB1 extrusion and reveal ERK-ZO-1 signaling as a key regulator of oocyte maturation.

cell biology↗

bioRxiv2026

Charting sex divergence in the human brain across the lifespan

Biological sex fundamentally shapes human brain organization, but sex-specific normative neuroanatomical trajectories across the lifespan remain largely uncharted. Here, we constructed independent, sex-specific lifespan brain charts using structural neuroimaging data from 59,915 healthy individuals (29,760 males and 30,155 females) ranging in age from 266 postconception days to 100 years. By examining 296 structural phenotypes across global, cortical, and subcortical measures, these models revealed widespread sex differences in maturational timing, with males reaching peak milestones later than females. These trajectories demonstrate that sex differences evolve dynamically, with phenotype-specific windows of emergence and maximal separation. Compared with conventional sex-pooled references, sex-specific models achieved superior predictive accuracy and reduced misestimation of individual deviations in healthy populations. Across five neuropsychiatric conditions, sex-specific models improved the detection of extreme deviations and revealed both shared and sex-dependent patterns of disorder-related neuroanatomical abnormalities. These sex-specific charts establish tailored normative references for assessing brain development, ageing, and disease.

neuroscience↗

bioRxiv2026

FLASH X-rays preserve neutrophil chromatin to boost antitumor immunity

Ultrahigh dose-rate FLASH radiotherapy spares normal tissue while preserving antitumor activity, positioning it as a promising technology in radiation oncology, but its immunomodulatory mechanisms remain elusive. Here, using a bilateral subcutaneous tumor model in mice, we show that 8-Gy FLASH X-rays, versus an equal dose of conventional dose-rate (CONV) X-rays, elicit a robust abscopal antitumor effect with anti-PD-1 therapy. Single-cell transcriptome and T cell receptor (TCR) profiling reveal that FLASH X-rays plus anti-PD-1 enhance antitumor immune infiltration and TCR clonal expansion in both irradiated and abscopal tumor lesions. Mechanistically, the ultrashort temporal continuity of FLASH dose delivery conserves chromatin compaction in neutrophils during exposure and inhibits neutrophil extracellular trap (NET) formation, thereby dismantling NET-mediated CD8+ T-cell exclusion within primary tumors. Conversely, CONV or split-dose FLASH X-rays induce marked chromatin modifications prior to dose completion, leading to chromatin hyper-relaxation which promotes NETosis and consequently abrogates systemic antitumor immunity. Notably, this detrimental effect can be reversed by pharmacologically suppressing PARylation-mediated chromatin modification and decondensation in neutrophils. These findings identify radiation-induced aberrant chromatin relaxation in neutrophils as a critical determinant of radioimmunotherapy outcomes, providing a rationale for redefining the FLASH effect and advancing its clinical translation.

cancer biology↗

bioRxiv2026

High temperature ligation enables in vitro assembly of eukaryotic genes

Our ability to efficiently construct synthetic DNA products is essential to studying and engineering biology. There is an abundance of widely adopted DNA assembly technologies suitable for generating synthetic constructs from diverse DNA inputs, but these techniques suffer from low specificity of connection during assembly, which decreases the accuracy, efficiency, and throughput of construction. Here we propose a broadly applicable paradigm for DNA assembly, High Temperature (HighT) assembly, that lowers misconnection rates by ligating complementary single strand DNA overhangs at reaction temperatures significantly higher than their predicted melting temperatures. By expanding the concept of melting temperature to demarcate smaller association fractions of DNA duplexes, we characterize HighT and demonstrate 40 percentage points increase in accuracy, and 4 orders of magnitude increase in yield of transformants when applying the technique to conventional assembly technologies. HighT is then applied to develop cloning pipelines for the development of efficient assembly-to-integration protocols, the construction of specific low-abundance isoforms of medically relevant proteins from human gDNA and oligos, and the de novo construction of a 10 kb, GC rich genomic region from the functionally extinct Northern White Rhinoceros created entirely in vitro.

molecular biology↗

bioRxiv2026

Autonomic neurons are intrinsically hyperexcitable in a Friedreich ataxia iPSC model

Friedreich ataxia (FRDA) is an inherited multisystem disorder caused by a GAA repeat expansion in the FXN gene and consequent frataxin deficiency, causing progressive neurodegeneration and heart disease. Clinical studies have documented autonomic dysfunction in FRDA, including elevated resting heart rate, raised plasma catecholamines and a high burden of urinary, bowel and sexual symptoms. Consistent with this, autopsy studies show degeneration of the cardiac conduction system and its associated ganglia in FRDA. Whether these features are intrinsic to FRDA autonomic neurons has been untestable without a human cellular model. Here, a human model of FRDA autonomic neurons was established by differentiating induced pluripotent stem cells (iPSCs) from individuals with FRDA and from their CRISPR/Cas9-corrected isogenic controls. FRDA autonomic neurons expressed canonical autonomic lineage markers and retained reduced FXN mRNA and frataxin protein levels. Electrophysiological analysis revealed pronounced hyperexcitability, with an approximately five-fold increase in spike number, shortened interspike intervals, and longer bursts. FRDA autonomic neurons also exhibited increased cell death, elevated mitochondrial reactive oxygen species, and a shift from networked to tubular mitochondrial morphology. Bulk RNA sequencing of all three isogenic pairs revealed loss of extracellular matrix programs and activation of stress response pathways. The top differentially expressed gene was MEG3, a maternally imprinted long noncoding RNA, which was consistently upregulated across all three isogenic pairs. MEG3 sits within the imprinted 14q32 DLK1-DIO3 locus, whose maternally expressed noncoding transcripts were co-ordinately de-repressed in FRDA autonomic neurons. Competitive gene-set testing of 43 imprinted genes across 20 domains showed this to be specific to 14q32: no other imprinted domain was co-ordinately altered. Together, these findings establish hyperexcitability of autonomic neurons as a cell autonomous consequence of frataxin deficiency, accompanied by mitochondrial dysfunction. This provides a cellular basis for the increased sympathetic tone observed in clinical studies.

neuroscience↗

bioRxiv2026

Impacts of different SETD1A mutations and genetic backgrounds on human induced pluripotent stem cell-derived hippocampal neurons

Abstract Human induced pluripotent stem cells (hiPSCs) provide a translational platform to interrogate the impact of genetic risk factors for various disorders on human biology. It has been a common practice to engineer premature stop codons to model predicted loss-of-function mutations using isogenic hiPSCs, yet effects of mutation position for the same gene and genetic background have been rarely tested systematically and at multiple levels for comparison to those of patient-specific mutations. Ultra-rare, heterozygous, and predicted loss-of-function mutations in the SETD1A gene, which encodes a H3K4 methyltransferase, are highly penetrant genetic risk factors for schizophrenia. Here, we generated a large panel of isogenic heterozygous SETD1A mutant hiPSC lines, including premature stop-codon mutations in one early exon and one late exon in five genetic backgrounds and two patient-specific mutations, to gain insight into molecular, cellular, and functional changes in a disease-relevant and highly pure population of human hippocampal dentate granule cell-like neurons. Our multi-level analyses showed that different SETD1A mutations lead to divergent molecular and cellular phenotypes related to synapses, but convergent neuronal network deficits, while the genetic background influences gene expression with no substantial effects at cellular and network levels. Mechanistic analysis confirmed the early exon patient mutation as loss-of-function, but revealed that the predicted loss-of-function patient mutation in the late exon is likely gain-of-function. Consequently, while all mutations decreased global H3K4me3 levels, deficits were only partially rescued by inhibiting H3K4 demethylase LSD1 for early exon mutations, but not for late exon mutations. Together, these results suggest that highly penetrant mutations can lead to similar cellular and functional phenotypes across different genetic backgrounds, whereas different premature stop-codon mutations could have contrasting impacts due to distinct mechanisms. Our findings have practical implications for applying genome-editing in hiPSCs to model disorders, highlight the value of modeling patient-specific mutations and testing multiple mutations, and suggest the need for tailored mutation-dependent therapeutic strategies.

neuroscience↗

bioRxiv2026

Defense-associated reverse transcriptases synthesize DNA in a telomerase-like manner

Defense-associated reverse transcriptases (DRTs) constitute an emerging class of bacterial defense systems that harness reverse-transcriptase activity to generate cDNA products and counter phage infection. A distinct subset of DRT10 systems evolutionarily related to telomerase generates tandem-repeat DNA to confer antiphage immunity. Here, we biochemically characterize the reverse transcription activity of DRT10 and determine cryo-EM structures of DRT10-ncRNA complex in three functional states, revealing an unanticipated 2:1 RT:ncRNA assembly mode. Two DRT10 protomers dimerize through a central pair of interlocked {beta}-hairpins and are further embraced by a single ncRNA. This architecture distinguishes DRT10 from previously characterized DRT complexes, which either lack an ncRNA component or exhibit an equivalent stoichiometry of RT:ncRNA. Strikingly, despite the nearly identical conformations of the two DRT10 protomers, cDNA product density was resolved in only one catalytic pocket, revealing different product occupancy within the dimer. Moreover, along with flanking linkers, the stem loops of the ncRNA as fixed points to supply steric barriers help define the template boundary. These findings reveal a distinctive ncRNA-mediated DRT10 dimeric assembly and establish a mechanistic framework for protein-primed reverse transcription constrained by the length of the RNA flanking linker.

biochemistry↗

bioRxiv2026

PaleoRigor: a bounded research agent with a reproducible evidence trail for paleomicrobiome data processing

Background: Ancient microbial evidence informs research on past health, diet, and environments, but its scarcity and susceptibility to contamination demand care in selecting and processing data. Language models can now turn a research request into an analysis plan, but an unconstrained planner may reference files that do not exist, apply operations a format forbids, or answer a question the data cannot settle. A planner used on such evidence therefore needs to be bounded, and its decisions recoverable afterwards. Results: We developed PaleoRigor around three commitments. Agent: a language model plans the analysis. Constraint: a validator checks every file reference, format and step dependency before anything runs, execution is restricted to predefined local modules, and a planning contract directs the model to refuse out-of-scope requests with a named reason code rather than answer them. Reproducibility: each run is exported with its plan, intermediate files, checksums and decisions. In a preregistered, frozen held-out evaluation, PaleoRigor passed 23 of 24 runs (95.8%; Wilson 95% confidence interval, 79.8-99.3%): 11 of 12 supported runs and all 12 prespecified boundary decisions. An ablation that removed this planning contract from the same model passed 19 of 24 (79.2%). Repeating the frozen design with a second model configuration yielded 24 of 24 successes for PaleoRigor and 19 of 24 for the ablated arm. Pooled post hoc across both configurations, PaleoRigor passed 47 of 48 runs (97.9%), compared with 38 of 48 (79.2%) for the ablated arms. All 96 run labels were recomputed from retained records and matched. Dataset-level tests matched read counts and compressed-file sizes for six public sequencing records and documented the removal of 114 duplicate sequence entries. A retraction-associated audit illustrated how expert review limited conclusions to file-level evidence. Conclusions: For paleomicrobiome data, pairing a language-model agent with explicit constraints and a reproducible record makes the agent's proposed analysis reviewable before its outputs support a biological claim. PaleoRigor delivers checked inputs, a recorded transformation history and a named reason for each request it refuses, and runs as a local desktop application. It prepares data for specialist analysis; ancient-DNA authentication and biological interpretation remain with the paleobiologist.

bioinformatics↗

bioRxiv2026

Long-range transport of biomolecular condensates by Marangoni effect

How mesoscale cargos such as biomolecular condensates are transported and spatially positioned within cells remains a fundamental question in cell biology. During Caenorhabditis elegans zygote polarization, a substantial fraction of P granules undergoes persistent anterior-to-posterior motion that cannot be fully explained by dissolution-recondensation. Here, combining microfluidic reconstitution, quantitative micropipette aspiration and live-cell imaging, we show that a MEG-3 concentration gradient generates interfacial-tension asymmetry and drives the directed transport of PGL-3-RNA co-condensates in vitro and P granules in vivo through the Marangoni effect. This framework enables parameter-free quantitative predictions of condensate transport. Orthogonal molecular perturbations abolish or reverse directional migration, directly linking interfacial properties to transport behavior and establishing the specificity of this mechanism. Together, our findings identify the Marangoni effect as a previously unrecognized mechanism for intracellular transport of biomolecular condensates and provide direct causal evidence that condensate emergent properties can contribute to physiological organization.

biophysics↗

bioRxiv2026

The multiscale architecture of trait aggression: from meta-analytic convergence to multimodal characterization

Background. Trait aggression shows substantial interindividual variability, yet its neurobiological architecture across structural, functional, molecular, and macroscale organizational levels remains poorly understood. Methods. We developed a convergent multiscale framework to characterize the neurobiological architecture associated with trait aggression. We first integrated a large-sample voxel-based morphometry analysis (n = 922) with published neuroimaging studies using two complementary coordinate-based meta-analytic approaches, activation likelihood estimation and seed-based d mapping (total N = 3,671). Convergent meta-analytic findings were subsequently mapped onto functional connectivity networks, and their molecular signatures were characterized using imaging transcriptomics and neurotransmitter mapping. Finally, we examined whether the spatial organization of aggression-related networks was embedded within intrinsic multimodal brain hierarchies spanning morphometric, functional, transcriptomic, and neurochemical dimensions. Results. Across complementary analyses, trait aggression converged on a reproducible structural-functional network centered on the dorsomedial prefrontal cortex and dorsal anterior cingulate cortex. This architecture exhibited distinct molecular signatures, including gene-expression patterns enriched for synaptic functions and robust spatial associations with serotonergic, dopaminergic, and noradrenergic transporter systems. Moreover, the spatial organization of the aggression-related functional network was systematically predicted by the brain's intrinsic multimodal gradients, indicating that it is embedded within broader principles of cortical hierarchical organization. Conclusions. these findings move beyond the localization of aggression to discrete brain regions and identify a reproducible multiscale architecture linking aggression-related structural variation to functional network organization, molecular signatures, and the brain's intrinsic multimodal hierarchy. This integrative framework provides a systems-level account of the neurobiological basis of individual differences in trait aggression.

neuroscience↗

bioRxiv2026

Causal evidence for the role of dorsolateral prefrontal cortex in the implementation of cognitive control adjustments

Cognitive control processes enable us to use recent contextual information to flexibly adapt to current task demands. This ability to adapt control processes is exhibited in response conflict tasks. In these tasks, participants must respond to a relevant piece of information while overcoming the tendency to respond to task-irrelevant information that cues an automatic or habitual response. Control demands can be updated in these tasks via two separate routes. Both errors and conflict between task-irrelevant and task-relevant information affect performance on subsequent trials. A body of work has implicated dorsolateral prefrontal cortex (DLPFC) in implementing these control adjustments. However, this work has primarily relied on correlational techniques or focused on a single index of control adaptation. Here, we combine inhibitory transcranial magnetic stimulation (TMS) over DLPFC with computational modeling of behavior to test the causal role of DLPFC in control adaptation. We show that inhibitory TMS to DLPFC reduces the effect of previous trial conflict, and committing an error on the previous trial further reduces adaptive effects. This result provides causal evidence for DLPFC playing a general role in implementing trial-to-trial control adjustments.

neuroscience↗

bioRxiv2026

TRIM21 licenses pancreatic acinar fate by modulating BiP phase state through VCP-dependent retrotranslocation

The endoplasmic reticulum (ER) chaperone BiP/GRP78 sits at the center of the proteostasis network, coordinating unfolded protein response (UPR) signaling and supporting oncogenic programs of plasticity, metastasis, immune evasion, and chemoresistance. While BiP undergoes liquid-liquid phase separation in vitro, whether mammalian cells dynamically tune this physicochemical behavior to prevent functional exhaustion or pathological condensation under sustained ER stress has remained unclear. Here, we identify the E3 ubiquitin ligase TRIM21 as a phase-state regulator that suppresses BiP's liquid-to-solid phase separation, clearing, and preventing insoluble aggregates-thereby controlling BiP's localization and availability to sustain the adaptive UPR under ER stress. We found that during ER stress, BiP is prone to liquid-to-solid phase separation, a transition that renders the chaperone dysfunctional. TRIM21 is recruited to BiP, where it directly polyubiquitinates BiP at specific K547/553/554/556 sites with K6-, K27-, K33-, and K63-linked chains; VCP recognizes these marks and extracts BiP from the ER lumen via ER-associated degradation (ERAD), coupling ubiquitin tagging to retrotranslocation. This preserves chaperone availability and sustains adaptive UPR-a homeostatic mechanism broadly relevant to UPR-driven diseases. In vivo, genetic ablation of Trim21 in KrasG12D/+; Pdx1Cre/+ mice triggers aberrant BiP solidification while curtailing acinar-to-ductal transdifferentiation and tumorigenesis; notably, TRIM21 co-localizes with BiP condensates in pre-malignant human pancreatic lesions, underscoring the clinical relevance of this regulatory axis. Our findings define the TRIM21-BiP axis as a phase-control system at the interface of proteostasis and stress adaptation, offering a new framework with translational potential.

cell biology↗

bioRxiv2026

VPS34 regulation in pulmonary arterial vascular smooth muscle cells in pulmonary hypertension

Pulmonary arterial hypertension (PAH) is characterized by the hyperproliferative phenotype of pulmonary arterial smooth muscle cells (PAVSMCs) and extensive extracellular matrix (ECM) remodeling. Vacuolar protein sorting 34 (VPS34), a Class III Phosphatidylinositol-3 Kinase (PI3K), regulates cell proliferation, but its specific function in pulmonary vascular remodeling remains poorly understood. We aim to determine the role of VPS34 activation and regulation in PAVSMC proliferation, matrix deposition, and the progression of PAH. First, we found a marked decrease in the inhibitory phosphorylation of VPS34 at Ser164 (P-S164-VPS34), indicative of constitutive VPS34 activation, in remodeled pulmonary arteries (PAs) from human PAH patients and male mice exposed to Sugen/Hypoxia (SuHx). In human PAH PAVSMCs, siRNA-mediated knockdown of VPS34 or pharmacological inhibition via the selective inhibitor SAR405 significantly blunted cell proliferation and reduced the production of fibronectin, a major component of the remodeled ECM. Mechanistically, we found that Akt activation in PAH PAVSMCs promotes VPS34 activation; Protein Phosphatase 1 Catalytic Subunit Alpha is a potential effector in VPS34 activation; and active VPS34 led to the activation of the mTOR/S6 signaling pathway with tuberous sclerosis complex 2 downregulation. Finally, in vivo treatment with SAR405 attenuated right ventricular systolic pressure, right ventricular hypertrophy, and pulmonary vascular remodeling in SuHx mice, while concurrently decreasing vascular fibronectin deposition. Our study demonstrates that VPS34 activation, driven by an Akt-mediated loss of the inhibitory P-S164, is crucial in PAVSMC proliferation and fibrotic vascular remodeling in PAH. Targeting the VPS34 axis represents a promising anti-remodeling therapeutic strategy for the treatment of PAH. Keywords: Pulmonary arterial hypertension, vacuolar protein sorting 34, pulmonary vascular remodeling, pulmonary arterial vascular smooth muscle

cell biology↗

bioRxiv2026

Reconstitution of +1 nucleosome transcription reveals coordinated functions of SAGA, Mediator, and TFIIH

The +1 nucleosome has emerged as a key regulator of eukaryotic transcription, but how it controls transcription initiation remains poorly understood. Here we reconstitute transcription through the +1 nucleosome using eleven purified yeast factors: RNA polymerase II (Pol II), the six general transcription factors (GTFs), TFIIS, the activator Pho4, and the SAGA and Mediator complexes. The system recapitulates key features of regulation observed in vivo. SAGA, acting with Pho4, directs pre-initiation complex (PIC) assembly to the correct position through its TBP-loading activity. Mediator stimulates transcription when the +1 nucleosome imposes a barrier to PIC formation, consistent with stabilization of productive TFIIH-DNA engagement. Contrary to the prevailing model, SAGA remains bound to the PIC after TBP loading and acetylates the +1 nucleosome within the assembled complex. The isolated PIC-Mediator-SAGA-nucleosome complex is transcriptionally active, and the repressive effect of the nucleosome is relieved by the DNA translocase activity of Ssl2, the TFIIH subunit that opens promoter DNA. TFIIH thus couples promoter melting to remodeling of the +1 nucleosome.

biochemistry↗

bioRxiv2026

UniWave-2: A Hybrid Model for Nucleic Acid Waveform Feature Extraction Enhanced by Fourier and Wavelet Transforms

Motivation: Traditional methods primarily rely on statistical features such as k-mers and GC content, making it difficult to capture complex internal relationships within sequences. Deep learning models typically rely on discrete encodings, leading to issues such as information sparsity, dimensional redun-dancy, and disruption of sequence continuity. Our previous UniWave-1 framework transforms se-quences into waveform signals; however, it lacks comprehensive physicochemical integration and com-putational efficiency. Results: We propose the UniWave-2 feature extraction framework. UniWave-2 incorporates three key advancements: (i) integration of hydrophobicity into the encoding scheme; (ii) enhancement of wave-form resolution through Fourier transform, coupled with wavelet transform to precisely capture both local details and global periodic patterns; and (iii) development of a lightweight multi-scale GRU model that facilitates cross-dimensional feature interactions, captures bidirectional temporal dependencies, and integrates long- and short-range patterns with spatial positional awareness, thereby yielding rich feature representations. UniWave-2 achieved competitive performance across multiple genomic tasks, while ISM analysis demonstrated that waveform encoding enables interpretable attribution without re-lying on gradient information. These results establish UniWave-2 as a lightweight and interpretable framework for nucleic acid sequence analysis.

bioinformatics↗

bioRxiv2026

Brain state shapes the polarity of pulsed infrared neural stimulation responses in individual cortical neurons

Pulsed infrared neural stimulation (INS, 1875nm the peak of energy absorption by water) is a non-viral method developed to activate single submillimeter sites in the brain. When used in ultrahigh-field fMRI, it reveals functionally specific brain-wide columnar networks comprising synaptically activated nodes. INS is non-damaging and effective for use in the human cortex and is useful for neural and behavioral neuromodulation in primates. To investigate how physiological state influences its cellular effects, we performed in vivo two-photon calcium imaging with GCaMP6s in mice and tracked identified cortical neurons in awake vs anesthetized states. Across the tested radiant exposures, INS-evoked responses differed markedly between states: under anesthesia, stimulation produced predominantly positive-going calcium responses, whereas during wakefulness the same identified neurons exhibited negative-going responses. Pharmacological manipulation of this baseline level by GABAergic signaling shifted response polarity in opposite directions: picrotoxin under anesthesia produced awake-like negative responses, whereas muscimol during wakefulness produced anesthetized-like positive responses. Trial-by-trial analyses further showed that the relationship between pre-stimulus baseline level and INS-evoked response depended on physiological state. Because INS relies on transient tissue heating, we also developed an in situ EGFP-based calibration approach to estimate temperature-related fluorescence changes. These fluoro-thermal contributions were modest at lower radiant exposures and became increasingly important at higher exposures, particularly near the fiber pathway. The low-intensity results are consistent with, but do not establish, a state-dependent feed-forward inhibitory framework. Together, these findings show that the neuronal response to focal INS is shaped by ongoing brain state and provide a practical framework for separating state-dependent calcium responses from temperature-related fluorescence effects, making INS a potentially versatile tool for neuroscience and clinical applications.

neuroscience↗

bioRxiv2026

Deciphering Mechanistic Signatures in Drug-Drug Interactions with Dual Topology Graphs

Drug-drug interactions (DDIs) represent a critical challenge in drug development and clinical practice, as they can lead to severe adverse effects, including toxicity and reduced therapeutic efficacy. Deep learning methods have shown promise in large-scale, rapid DDI prediction; however, current approaches suffer from significant limitations in providing mechanistic insights into these interactions. Here, we propose DualTopoDDI, a dual-topology-enhanced interpretable deep learning model for DDI prediction. We applied DualTopoDDI to predict 9.2 billion potential interactions among approved drugs, achieving 97.99% high-confidence predictions. The model demonstrates molecular-level interpretability, identifying key substructures responsible for drug actions in terms of both atom-centric and bond-centric views. DualTopoDDI also excels in elucidating particular DDI toxicity mechanisms, which is validated by its successful explanation of the controversial cardiac toxicity in two COVID-19 drug combination regimens at the time. Evaluations across 11 benchmark datasets demonstrates that DualTopoDDI not only achieves state-of-the-art performance but also showcases robust generalizability and good interpretability. Overall, DualTopoDDI offers a powerful, interpretable tool for understanding and predicting drug-drug interactions, providing critical insights for drug safety and design.

bioinformatics↗

bioRxiv2026

Temporal TOC1-CLV3-WUS cascade controls organogenesis and rhythmic stem development

Coordinated organogenesis and rhythmic stem development determine shoot morphogenesis, which governs distinct plant architecture and crop yield. The shoot apical meristem (SAM) drives organ initiation and stem growth, with its activity sustained by the spatially defined CLAVATA3 (CLV3)-WUSCHEL (WUS) feedback loop. However, how the temporal CLV3-WUS module modulates SAM activity remains elusive. Here, we demonstrate that both CLV3 and WUS are required for circadian stem elongation. The clock component TIMING OF CAB EXPRESSION1 (TOC1) directly activates and sustains the circadian expression of CLV3, and this regulatory process is controlled by the APETALA1-CIRCADIAN CLOCK-ASSOCIATED1 module. Notably, the rhythmic expression pattern of CLV3, rather than its transcript abundance, plays a more important role in regulating WUS expression and sustaining SAM activity, and CLV3 confers circadian rhythmicity to WUS protein accumulation. Transcriptome and ChIP seq analyses reveal that WUS modulates multiple developmental programs, including meristem homeostasis, phytohormone responses, and cell wall remodeling. Mechanistically, WUS directly activates PECTIN METHYLESTERASE5 expression to promote stem elongation. Collectively, our findings uncover a spatiotemporal regulatory cascade that fine-tunes SAM activity to coordinate rhythmic organogenesis and stem development, thereby establishing optimal phyllotactic patterning in plants.

plant biology↗