Biology subjects

Dong, W.

Publications and source records attributed to Dong, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Epithelial-Mesenchymal Wnt Crosstalk Directs Planar Cell Polarity in the Developing Cochlea

Cochlear hair cells are crucial for sound transduction and are precisely oriented by planar cell polarity (PCP). Wnt proteins direct PCP in vertebrates, but their roles in regulating cochlear PCP remain unclear. Here, we inhibited Wnt secretion by ablating Wntless in the cochlear epithelium and found shortened cochlea, mild hair cell misorientation and mislocalization of PCP proteins, Fzd6 and Dvl2, representing defects less severe than classic PCP mutants. Computational cell-communication analysis predicted that candidate Wnts from the cochlear epithelium (Wnt5a, Wnt7a, Wnt7b) and surrounding periotic mesenchyme (Wnt5a) act on developing hair cells. Deletion of Wnt5a, Wnt7a, and Wnt7b additively shortened the cochlea without causing hair cell misorientation or mislocalization of PCP proteins. Moreover, deletion of Wnt5a alone in the periotic mesenchyme failed to cause PCP defects. However, ablating both epithelial and mesenchymal Wnts caused a severely shortened cochlea with apically malrotated hair cells devoid of polarized core PCP proteins. Thus, Wnts serve as global instructive cues directing cochlear outgrowth and hair cell polarization, with remarkable redundancy of distinct Wnts across epithelial and mesenchymal compartments to ensure a fail-safe developmental program.

developmental biology↗

bioRxiv2026

Near completely reversing the γ- to β-globin switch by enhancer release, retargeting and reinforcing

The {gamma}- to {beta}-globin switch is intricately regulated during human ontogeny, and this process is manipulated for therapeutic approaches to treat {beta}-hemoglobinopathies by activating {gamma}-globin expression. Several genetic strategies to reactivate HbF have partially reversed the {gamma}- to {beta}-globin switch and ameliorated the clinical symptoms of {beta}-hemoglobinopathies. However, whether the {gamma}- to {beta}-globin switch can be completely reversed remains unknown. Completely reversing the {gamma}- to {beta}-globin switch requires a thorough redirection of the locus control region (LCR) from interacting with the {beta}-globin gene (HBB) to interacting with the {gamma}-globin gene (HBG). Here, we found that disrupting the KLF1-mediated HBB-LCR interaction by mutating the CACCC motif in HBB leads to the release of the LCR and its retargeting to other {beta}-like globin genes. Moreover, simultaneously disrupting the KLF1-mediated HBB-LCR interaction and the epigenetic repression of HBG by combined editing of the CACCC motif in HBB and the TGACCA motif in HBG reinforces the HBG-LCR interaction, resulting in almost exclusive {gamma}-globin expression while nearly absent {beta}-globin expression, achieving near complete reversal of the {gamma}- to {beta}-globin switch. This finding demonstrates the comprehensive regulation of the {gamma}- to {beta}-globin switch by gene competition and gene silencing mechanisms. This finding also suggests that silenced genes can be fully activated through the redirection of enhancer-promoter contacts and that the specificity of enhancer-promoter contact within chromosomal domains is achieved through the transcription factor clusters binding to enhancers and promoters. Combined editing of the CACCC&TGACCA motifs also offer a more optimal therapeutic strategy for {beta}-hemoglobinopathies.

molecular biology↗

bioRxiv2026

Shared and distinct default mode systems in mental time travel and affective experience over time

Overarching conceptualizations propose a critical role of the default mode network (DMN) in self-referential mental time travel, particularly in autobiographical memory retrieval and episodic future thinking, and internal (intrinsic) emotion generation and regulation. However, these conceptualizations have not been directly evaluated. Against this background, the present fMRI study aimed to identify both shared and distinct neural systems underlying autobiographical episodic processing across different temporal contexts - specifically, episodic memory retrieval (EMR) and episodic future thinking (EFT) - and to examine how these systems interact with affective experiences, including valence and arousal. Our findings demonstrated the central role of the DMN - encompassing the medial prefrontal cortex (mPFC), posterior cingulate cortex (PCC), and medial temporal lobe (MTL) - in both EMR and EFT. Importantly, we identified a functional dissociation along both valence and temporal dimensions: the ventromedial prefrontal cortex (vmPFC) was more strongly associated with positive experiences and simulations, whereas the dorsomedial prefrontal cortex (dmPFC) was consistently engaged during the processing of negative affect across past and future contexts. Moreover, representational similarity and parametric analyses indicated that the hippocampus supports differential processing of valence and arousal across temporal domains. Together, these findings provide empirical evidence for the involvement of cortical midline core DMN systems in autobiographical processing across time and suggest overlapping and distinct systems for the integration of emotional experiences across mental time travel.

neuroscience↗

bioRxiv2025

Tryptophan-substitution antimicrobial peptide temporin-1CEb: in vitro and in vivo antibacterial activity against clinically isolated multidrug-resistant Klebsiella pneumoniae

Tryptophan (Trp)-substitution antimicrobial peptides (AMPs) exhibit enhanced interactions with bacterial cell membranes, potentially improving their antimicrobial efficacy. K. pneumoniae (20.59% of 2054 ICU isolates) is resistant to multiple clinically used antibiotics and presents significant treatment challenges. In the present study, three Trp-modified peptides (I4W, L12W, and I1WL5W) were generated by substituting Ile or Leu residues in temporin-1CEb, a peptide derived from frog skin, with Trp at various sites to assess their antibacterial effects and mechanisms against K. pneumoniae. Compared with L12W, both I4W and I1WL5W displayed superior antimicrobial activity and lower cytotoxicity. Mechanistic studies revealed that the AMPs exerted antibacterial and bactericidal effects through bacterial surface charge neutralization, insertion into bacterial cell membranes, increased permeability of both the inner and outer membranes, and disruption of membrane integrity. Notably, I1WL5W exhibited the most potent membrane-disrupting activity. Assessment of the impact of Trp-containing peptides on bacterial biofilms revealed that these peptides not only inhibited exopolysaccharide production and biofilm formation but also degraded preformed biofilms. A murine lung infection model was established to investigate the therapeutic efficacy of I1WL5W against MDRKP 1203-induced lung infection in mice. Compared with the control treatment, treatment with I1WL5W resulted in reduced bacterial counts and levels of IL-6 and TNF- in both the blood and lung tissues of MDRKP 1203-infected mice, and treatment with I1WL5W improved lung tissue structure. The present study provides valuable insights for designing Trp-containing peptides with potent antimicrobial properties by facilitating their penetration across bacterial membranes.

pharmacology and toxicology↗

bioRxiv2025

HINS: HLA-mediated immunogenic neoantigen score for robust prediction of immune checkpoint blockade response

Immune checkpoint blockade (ICB) therapy response prediction provides remarkable genomic and transcriptomic gains and has successfully understood the molecular mechanisms underlying various cancers. However, only a subset of patients with advanced tumors currently benefits from ICB therapies, which at times incur considerable side effects and costs. Developing predictive tools for ICB response has remained a serious challenge because of the complexity of the immune response and the shortage of large cohorts of ICB-treated patients that include both omics and response data. Here, based on a pooled genomic dataset of 919 patients across multiple solid tumors treated with anti-PD-(L)1 or anti-CTLA-4, we constructed human leukocyte antigen class I (HLA-I)-mediated immunogenic neoantigen score (HINS). HINS is a predictor of ICB response using neoantigen quality and HLA evolutionary divergence to integrate the factors associated with immune activation and evasion. It yielded an overall accuracy of AUC=0.853, outperforming existing predictors and capturing more than 75% true responders. Experimental analysis indicated that patients with higher HINS were more likely to undergo survival benefits following ICB therapy. Our results highlighted the transcriptional and genomic correlations between HINS-identified molecule features and ICB response, such as immunoresponsive gene enrich pathways, favorable and unfavorable genomic subgroups, and hotspot somatic events in driver genes. This study presented an interpretable, accurate deep-learning method using meaningful predictive features to predict the response to ICB, providing biological insights into the complexity of the determinants underlying immunotherapy.

bioinformatics↗

bioRxiv2025

Warming winter disrupts mycorrhizal phenology and plant-fungal nutrient cycling.

Climate change is reshaping the timing of ecological processes in montane ecosystems, where short, snowpack-dependent growing seasons tightly constrain plant-microbe interactions. Arbuscular mycorrhizal (AM) fungi regulate plant acquisition of nitrogen (N) and phosphorus (P) during nutrient pulses triggered by melting snowpack. Yet the extent and consequences of warming-induced phenological asynchrony between AM fungi and host plants remains unknown. We experimentally advanced snowmelt in a subalpine meadow and monitored plant and AM fungal growth, soil nutrients, and AM fungal community composition throughout the growing season. Early snowmelt advanced plant greenness and root standing stock but suppressed AM fungal hyphal production, reducing available NH{square}{square} and PO43-. Hyphal allocation strategies shaped AM fungal temporal niches and species-specific responses to warming. Nutrient-foraging, edaphophilic AM fungi dominated early in the season, while rhizophilic AM fungi dominated later, following peak root growth. Our results reveal that fungal functional traits and nutrient dynamics govern the temporal niche partitioning of mycorrhizal fungi. By decoupling AM fungal activity from plant demand and nutrient mineralization windows, early snowmelt drives plant-fungal asynchrony. This decoupling weakens mycorrhizal symbioses and threatens nutrient retention and ecosystem stability under future warming. Such belowground temporal mismatches may determine the resilience of seasonally temperature-dependent ecosystems under warming.

ecology↗

bioRxiv2025

Orthogonal representational geometry in dACC underpins human hierarchical reasoning

Flexible adaptation requires inferring the causes of feedback and adjusting accordingly. When tasks are hierarchically structured with high-level rules governing low-level perceptual judgements, good performance requires hierarchical reasoning. Yet the computational and neural mechanisms underlying this process remain unclear. Here, building on Bayesian modelling and recurrent neural network simulation of hierarchical reasoning, we verified that such algorithm and representations are implemented in human dorsal anterior cingulate cortex (dACC). dACC encodes accumulated errors and perceptual difficulty to estimate high-level rule switch confidence. These two variables were represented along two separable dimensions, and could be approximated by Gaussian basis functions. Orthogonality between these two dimensions yielded an optimal two-dimensional representation for hierarchical reasoning. A closer-to-orthogonal representational geometry also predicted better performance. Together, these findings provide an integrated computational and neural representational basis for hierarchical reasoning.

neuroscience↗

bioRxiv2025

End-to-end high-throughput single-cell proteomics via SPRINT and dual-spray LC-MS

Single-cell proteomics (SCP) enables direct measurement of protein heterogeneity but remains constrained by throughput and limited applicability to primary tissues. Here, we present an integrated workflow developed to address both challenges. We engineered SPRINT, an AI-powered bioprinting platform that prepares more than 10,000 single cells per day, over tenfold faster than existing systems, while maintaining stability and enabling identification of over 6,000 proteins from individual HeLa cells. To expand analytical capacity, we further designed a dual-spray tandem direct injection (TDI) LC system that parallelizes non-analytical steps with peptide separation, doubling MS utilization efficiency and enabling 168 label-free SCP runs per day without sensitivity loss. Together with optimized tissue-dissociation protocols, this integrated workflow enabled creation of the first mouse tissue-derived SCP atlas, profiling >1,000 single cells across six organs. These advances establish SCP as a scalable platform ready for broad biological and biomedical applications.

systems biology↗

bioRxiv2025

A systematic comparison of cooperation and coordination across behavioural, psychological, and neural scales

Cooperation and coordination are the two fundamental mechanisms for enhancing social welfare. However, the intrinsic differences between the dynamics of cooperation and coordination remain elusive, particularly from an interpretable perspective that bridges behavioural, psychological, and neural scales. Here, we compare and analyze cooperation and coordination within a unified framework by assigning participants to an adjustable public goods game for iterated real-time interactions. By integrating model-free behavioural patterns and psychological intentions, we show that individuals are driven by increased flexibility and are more susceptible to peer influence in decision-making under cooperation. While under coordination, it is easier to reach the group consensus, inspiring individuals to stick more closely to their existing behavioural patterns and the default social norms. Furthermore, although peer punishment can enhance reciprocal contributions in all scenarios, the detailed impact and the resultant adverse phenomena (anti-social punishment) in cooperation and coordination are different. Notably, behavioural motive differences are also reflected in the neural responses recorded via fNIRS, in which coordination is associated with activation of the rTPJ and more consistent inter-brain synchronization in the dmPFC, while there is a negative correlation between dmPFC-rTPJ connectivity and contributions under cooperation. In addition, rTPJ during the punishment phase is significantly activated compared with the investment phase. Our study systematically reveals the fundamental differences between cooperation and coordination at the multi-scale levels, which not only deepens the understanding of reciprocal behaviour in social groups, but also provides a foundation for designing targeted incentive mechanisms.

animal behavior and cognition↗

bioRxiv2025

A Benchmark of Evo2 Genomic AI Models for Efficient and Practical Deployment

The rapid advancement of DNA foundation language models has brought about a transformative shift in genomics, allowing for the deciphering of intricate patterns and regulatory mechanisms embedded within DNA sequences. The genomic foundation model Evo2 demonstrates remarkable capabilities in decoding DNA functional patterns through cross-species pretraining. However, despite the great potential of Evo2 in basic genomics research, there is currently no clear and systematic guidance on its specific application scenarios, performance, and optimization directions in the field of tumor genomics, and its performance dependency on specialized hardware (such as FP8 precision on H800 GPUs) has not been empirically benchmarked. Here, we present a focused validation of Evo2 using two independent cancer genomic datasets (Bladder Urothelial Carcinoma and Ovarian Cancer), we tested the downstream tasks of Evo2, including the prediction of tumor pathogenic variants and the prediction of mutational effects, and compared its performance on A100 and H800 GPUs. The results show that critical importance of FP8 precision, enabling the H800 to achieve a 4x faster inference speed than the A100 with stable accuracy (AUC 0.88-0.95). The 7B-parameter model emerged as the top performer, whereas the 40B model experienced a severe performance drop (AUC to 0.48) on non-FP8 hardware like the A100. These findings empirically validated Evo2s hardware specifications and provided practical insights for researchers implementing the model with similar computational resources. Futhermore, our findings provide a framework for the application and optimization of downstream tasks of the DNA language model Evo2 in cancer, and can guide researchers in effectively applying it in genomic studies. Key PointsO_LIHardware Precision Impact: FP8 precision on H800 GPUs is critical for Evo 2s performance, enabling 4x faster inference than A100 (without FP8 support) while maintaining high accuracy (AUC 0.88-0.95). C_LIO_LIModel Scale Optimization: The 7B-parameter model outperformed larger variants (e.g., 40B), which suffered severe accuracy drops (AUC as low as 0.48) on non-FP8 hardware, highlighting a balance between efficiency and performance. C_LIO_LIPractical Guidelines: We provide a framework for deploying Evo 2 in cancer genomics, including hardware recommendations, dataset curation, and downstream task optimization--valuable for researchers with varied computational resources. C_LI

genomics↗

bioRxiv2025

GeoGAT-site: A Face-Centered Geometric Graph Attention Network for Protein-Protein Interface Prediction

Protein-protein interactions (PPIs) underpin the intricate machinery of cellular life, orchestrating processes from signal transduction to metabolic regulation, yet their precise interface prediction remains a cornerstone challenge in structural biology, demanding scalable computational paradigms that balance accuracy and efficiency. Herein, we present GeoGAT-site, a pioneering geometric graph attention network that leverages face-centered surface fingerprints extracted from three-dimensional protein architectures to forecast interaction sites. Diverging from conventional vertex-centric approaches, our face-centered methodology achieves a 3.64-fold acceleration in patch generation, mitigating computational bottlenecks while preserving granular surface descriptors. At its core, GeoGAT-site incorporates a bespoke attention mechanism that adaptively modulates inter-facial distances and normal vector orientations, synergistically integrating spatial geometries with physicochemical attributes for nuanced interface delineation. Harnessing a meticulously curated dataset of 150 million face-centered fingerprints from over 20,000 structurally diverse proteins, the model attains robust generalization across heterogeneous interaction motifs. Empirical validation on an independent cohort of 167 protein complexes yields a ROC AUC of 0.89, surpassing established benchmarks including MaSIF-site (0.845), SPPIDER (0.65), and PSIVER (0.63). By furnishing high-fidelity interface annotations, GeoGAT-site augments downstream structural modeling paradigms through targeted constraints, thereby providing a versatile scaffold for unraveling PPI dynamics with profound implications for therapeutic discovery, protein redesign, and molecular epistemology.

bioinformatics↗

bioRxiv2025

Two closed systems for long-term propagation of the marine tunicate Botryllus schlosseri isolated from natural seawater

Advanced methodologies for Botryllus schlosseri artificial seawater systems are needed to decrease dependency of large-scale culture on natural seawater and expand use of this important new model organism to more inland laboratories. We constructed two botryllid tunicate customized closed aquaculture systems, a static system consisting of lightly aerated jars fed with commercial filter feeder diet, and a recirculating aquaculture system (RAS) consisting of standard marine RAS components fed live microalgae and zooplankton diets. Initially, static tunicate culture yielded exponential growth in contrast to the RAS system, which yielded poor survival and negligible growth. Modifications were made to the RAS system to improve water treatment proficiency that greatly improved tunicate survival and growth. Experiments were performed isolating feed and water type as variables that differed between the static and RAS systems to evaluate their effects. A live feed combination achieved five-fold greater growth relative to a commercial concentrate diet. B. schlosseri maintained in optimized RAS water achieved two-fold faster growth relative to animals maintained with freshly prepared artificial seawater indicating that the RAS water was beneficial to the animals. Feeding frequency of the RAS system was increased from three times per week to daily. The RAS system and procedural modifications resulted in comparable growth rates in the static and RAS systems. Both optimized systems are suitable for long-term propagation and sustenance of botryllid tunicate populations supporting both sexual and asexual modes of reproduction with a current residence time of over 24 months.

zoology↗

bioRxiv2025

Proteome Dynamics Across the Blastogenic Cycle of Botryllus schlosseri Reveals Targets for Cell Immortalization

The colonial tunicate Botryllus schlosseri regenerates weekly through a cyclical process in which adult zooids are replaced by a new generation of buds. While this dynamic asexual development is a hallmark of the species, its molecular regulation remains poorly understood. This study presents the first comprehensive proteomic analysis of B. schlosseri blastogenesis at the individual zooid level, using data-independent acquisition mass spectrometry to quantify protein abundance across developmental stages. The results reveal extensive proteome remodeling between proliferating buds and degenerating zooids. Co-expression analysis identified stage-specific protein modules enriched for biosynthesis and cell cycle pathways in buds, and for apoptosis, catabolism, and metabolic remodeling in zooids. A focused comparison between takeover buds and takeover zooids uncovered distinct regulatory programs controlling proliferation and senescence. Key proteins, including CDK1, CDK2, HDAC2, and PCNA, were identified as candidate regulators of cell cycle progression. These findings provide a molecular framework for understanding regeneration in a basal chordate and offer protein targets that may enable cell cycle re-entry and long-term culture of tunicate primary cells. Summary StatementThis study maps proteome dynamics during the blastogenic cycle in Botryllus schlosseri, identifying candidate proteins that regulate cell proliferation and offer targets for tunicate cell line development.

developmental biology↗

bioRxiv2025

Medial preoptic area FoxO1 controls metabolic adaptation in a sexually dimorphic manner

The medial preoptic area (MPOA) of the hypothalamus is essential for metabolic adaptation to environmental challenges, though the molecular mechanisms underlying this process remain poorly understood. Here, we investigate the role of Forkhead transcription factor O1 (FoxO1), a key mediator of stress adaptation, in MPOA-dependent metabolic responses to temperature and nutritional changes. Our findings reveal sex-specific responses to both nutritional and temperature challenges. In female mice, but not males, a high-fat diet (HFD) challenge decreased FoxO1 expression in the MPOA. Specific deletion of FoxO1 in MPOA neurons (FoxO1-KOMPOA) had no effect on body weight under normal chow-fed conditions but protected females from HFD-induced obesity (DIO). These protected females exhibited increased lean mass, decreased fat mass, enhanced thermogenesis, increased energy expenditure, and reduced food intake under HFD conditions. They also showed enhanced cold-induced heat production at 6{degrees}C, though this effect vanished at thermoneutrality (30{degrees}C). The protection against DIO was abolished by ovariectomy (OVX) and was not restored by 17{beta}-estradiol supplementation, suggesting an estrogen-independent mechanism. Conversely, constitutive activation of FoxO1 in MPOA neurons (FoxO1-CAMPOA) increased DIO susceptibility in both sexes. Together, these findings demonstrate that FoxO1MPOA plays a crucial role in coordinating metabolic adaptation to nutritional and temperature challenges specifically in female mice.

physiology↗

bioRxiv2025

Prolonged non-suppressible viremia sustained by a clonally expanded, genomically defective provirus with an immune-evasive HIV protein expression profile

Antiretroviral therapy (ART) potently inhibits HIV replication but does not eliminate HIV proviruses integrated within the genomes of infected cells. Though ART normally suppresses HIV to clinically undetectable levels in blood, some individuals experience non-suppressible viremia (NSV) that is not attributable to suboptimal drug exposure (e.g. due to incomplete medication adherence or pharmacological issues) nor emerging HIV drug resistance, and that does not resolve following regimen modification. We now understand that NSV can originate from expanded cell clones harboring genetically identical proviruses that reactivate en masse to produce clinically detectable viremia. NSV can even originate from proviruses with genomic defects, particularly in HIVs major splice donor (MSD) site, that render the viremia non-infectious. But, because only a limited number of such cases have been described, all in HIV subtype B, the mechanisms that allow cells harboring such proviruses to produce prolonged viremia without being eliminated remain incompletely understood. We characterized a case of MSD-defective, replication-impaired NSV that lasted >4 years in an individual with non-B HIV. Our results reveal that proviruses with MSD deletions can persist by integrating into minimally differentiated CD4+ T-cell subsets that then give rise to the full spectrum of memory and effector subpopulations, and by exhibiting an HIV protein expression profile that would allow these cells to evade cellular and humoral immunity. Our results highlight the need to better understand the biological implications of persistent HIV protein and virion production by genomically defective, clonally expanded proviruses, and for clinical guidelines to acknowledge this type of viremia. ImportanceHIV cure efforts focus on eliminating the viral reservoir, strictly defined as cells harboring proviruses that can produce infectious HIV. But this definition excludes proviruses with defects in HIVs major splice donor site (MSD), which persist readily. Our results confirm that clonally expanded, MSD-defective proviruses can produce HIV transcripts, proteins and clinically-detectable viremia over long periods, underscoring the need to investigate the potential long-term biological consequences of these activities. Our findings also have clinical implications. Most HIV treatment guidelines dont acknowledge that persistent viremia during ART can originate from clonally-expanded proviruses, and all recommend that viremia >200 HIV RNA copies/mL be managed as virologic failure. Clear clinical frameworks should be developed to discriminate persistent viremia that is due to drug adherence, pharmacokinetics or emerging drug resistance (that is clinically actionable), from NSV (that is not). Genotyping of HIVs MSD could also help assess potential transmission risk during NSV.

microbiology↗

bioRxiv2025

THLANet: A Deep Learning Framework for Predicting TCR-pHLA Binding in Immunotherapy Applications

Adaptive immunity is a targeted immune response that enables the body to identify and eliminate foreign pathogens, playing a critical role in the anti-tumor immune response. Tumor cell expression of antigens forms the foundation for inducing this adaptive response. However, the human leukocyte antigens (HLA)-restricted recognition of antigens by T-cell receptors (TCR) limits their ability to detect all neoantigens, with only a small subset capable of activating T-cells. Accurately predicting neoantigen binding to TCR is, therefore, crucial for assessing their immunogenic potential in clinical settings. We present THLANet, a deep learning model designed to predict the binding specificity of TCR to neoantigens presented by class I HLAs. THLANet employs evolutionary scale modeling-2 (ESM-2), replacing the traditional embedding methods to enhance sequence feature representation. Using scTCR-seq data, we obtained the TCR immune repertoire and constructed a TCR-pHLA binding database to validate THLANets clinical potential. The models performance was further evaluated using clinical cancer data across various cancer types. Additionally, by analyzing divided complementarity-determining region (CDR3) sequences and simulating alanine scanning of antigen sequences, we unveiled the 3D binding conformations of TCRs and antigens. Predicting TCR-neoantigen pairing remains a significant challenge in immunology, THLANet provides accurate predictions using only the TCR sequence (CDR3{beta}), antigen sequence, and class I HLA, offering novel insights into TCR-antigen interactions. Author summaryT-cell receptor (TCR) recognition of peptide-human leukocyte antigen (pHLA) complexes is fundamental to immune responses. However, predicting their binding poses a significant challenge due to the intricate dynamics of their interactions. We developed THLANet, a novel deep learning model, to address this challenge by integrating the ESM-2 and Transformer-Encoder modules. This approach enhances sequence feature encoding, improving the models generalization capability and enabling accurate predictions of TCR-pHLA binding in clinical datasets. Using data processed from open-source databases, THLANet outperformed existing methods, such as PanPep and pMTnet, in precision-recall metrics across multiple epitopes. Additionally, THLANet demonstrates superior capability in identifying critical binding sites within 3D structures, providing structural insights into TCR-pHLA interactions. THLANet offers a robust framework for advancing immunotherapy research, with potential applications in the development of personalized medicine.

bioinformatics↗

bioRxiv2025

Noninvasive ultrasound targeted modulation of calcium influx in splenic immunocytes potentiates antineoplastic immunity attenuating hepatocellular carcinoma proliferation

The spleen, as the largest immune organ, plays a pivotal role in modulating immune responses, particularly in the context of carcinogenesis and tumor progression. Non-pharmacological manipulation, particularly splenic ultrasound stimulation (SUS), has demonstrated significant immunomodulatory efficacy in alleviating chronic inflammatory diseases, suggesting its potential to revitalize splenic immunocompetence suppressing tumor proliferation, yet remains underexplored. This study applied low-frequency pulsed focused ultrasound (FUS) noninvasively stimulating the spleen (FUS sti. spleen) to investigate the efficacy in enhancing antitumor immunity and suppressing hepatocellular carcinoma (HCC). The results showed that FUS sti. spleen significantly suppressed tumor proliferation, achieving a suppression rate of >70% for H22-HCC and >83% for Hepa1-6-HCC, along with significantly prolonged survival. Comprehensive flow cytometry, single-cell RNA sequencing (scRNA-seq) and cytokine analyses demonstrated that SUS profoundly reshaped the splenic and intratumoral immune landscape, specifically activating cytotoxic CD8+ T cells and NK cells while suppressing immunosuppressive cell populations. Mechanistically, FUS facilitated calcium influx in splenic immunocytes, activating multiple signaling pathways, such as TNF, NF{kappa}B, MAPK, HIF-1, and ErbB, thereby counteracting tumor-driven immunosuppressive polarization while potentiating robust immune activation that impedes malignant progression and neoplastic proliferation. Leveraging above insights, we developed spleen-targeted nanodroplets encapsulating bioavailable calcium ions (STNDs@Ca{superscript 2}), which, upon FUS stimulation, undergo cavitation-mediated controlled release of Ca{superscript 2}, further amplifying immunocyte activation and tumor suppression, achieving a remarkable H22-HCC suppression rate of over 90%. This study highlights the therapeutic potential of ultrasound-mediated splenic immunomodulation, both as a standalone intervention and in synergy with STNDs@Ca{superscript 2}, as a novel and noninvasive strategy for cancer immunotherapy.

biophysics↗

bioRxiv2025

AT1R and Integrin β3 Synergize to Drive Aortic Dissection via Non-Canonical Wnt/β-Catenin Signaling

Aortic dissection (AD), a life-threatening cardiovascular emergency, continues to impose high mortality due to insufficient therapeutic options, as monotherapy targeting angiotensin II type 1 receptor (AT1R) demonstrates limited clinical efficacy. Utilizing single-cell RNA sequencing, we identified integrin {beta}3 as a critical driver of AD progression, with expression levels positively correlated with disease severity. Histopathological validation in human AD specimens and a murine angiotensin II (AngII)-infusion model confirmed marked upregulation of integrin {beta}3 activation. Pharmacological blockade of integrin {beta}3 with Cyclo(-RGDfK) significantly attenuated aortic pathogenesis in vivo, reducing dissection incidence and aortic degeneration. Mechanistically, AngII-mediated AT1R activation induced formation of a receptor complex with integrin {beta}3, triggering its conformational activation. Transcriptomic profiling revealed that activated integrin {beta}3 potentiates vascular endothelial dysfunction by binding glycogen synthase kinase 3{beta} (GSK3{beta}), which stabilizes {beta}-catenin via a non-canonical Wnt signaling axis. This pathway drives endothelial barrier disruption, hallmarks of aortic wall destabilization in AD. Our findings unveil a previously unrecognized synergy between AT1R and integrin {beta}3, implicating aberrant Wnt/{beta}-catenin signaling as a nexus of endothelial injury in AD pathogenesis. These results advocate for a paradigm-shifting dual-therapeutic strategy concurrently targeting AT1R and integrin {beta}3 to restore vascular homeostasis, offering a mechanistically grounded approach to mitigate this lethal disease. This work bridges critical gaps in understanding AD pathophysiology and provides a transformative framework for precision therapeutics.

pharmacology and toxicology↗