Biology subjects

Zhang, X.

Publications and source records attributed to Zhang, X..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Astrocytes instructively regulate neuronal translation

Neuronal protein synthesis is essential for synaptic plasticity and long-term memory, yet whether its regulation is shaped by other cell types remains poorly understood. Here, we show that astrocyte-secreted proteins regulate global neuronal translation depending on astrocytic state. Astrocyte-conditioned medium (ACM) increased neuronal translation under basal conditions, an effect enhanced by astrocyte stimulation with the activity-dependent factor BDNF, whereas ACM from neurotoxic reactive astrocytes, a state linked to neuroinflammation and Alzheimers disease, suppressed neuronal translation. Across these conditions, neuronal mTORC1 activity consistently tracked with translational output, whereas the integrated stress response (ISR) acted through distinct, state-specific mechanisms that did not always track with neuronal translation. Furthermore, we identified astrocyte-secreted apolipoprotein E (APOE) and its associated cargo as a negative regulator of neuronal translation that contributed to the decreased translation induced by neurotoxic reactive astrocytes. We also found that astrocyte-secreted signals required neuronal endocytosis to influence translation and drove synaptic remodeling dependent on glutamatergic signaling and neuronal mTORC1 activity. Together, these findings identify astrocytes as active, instructive regulators of neuronal translation and synaptic structure, with implications for understanding how astrocyte dysfunction may disrupt the translational mechanisms underlying impairments in synaptic plasticity and long-term memory in neurodegenerative disease. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/741020v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@74ecborg.highwire.dtl.DTLVardef@1c620a0org.highwire.dtl.DTLVardef@881b8corg.highwire.dtl.DTLVardef@1c8b7e4_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Perturbation response decomposition enables biologically aligned generalization to unseen perturbations and cellular contexts

Predicting single-cell responses to genetic perturbations could reveal the vast combinatorial space of perturbations and cellular contexts that is infeasible to measure experimentally, yet current deep learning models generalize poorly and often fail to outperform simple baselines. Here we demonstrate that generalizability in perturbation prediction requires identifying and representing distinct components of cellular response rather than on increasing model complexity alone. We introduce a decomposition framework that explicitly separates transcriptional responses into global, perturbation-specific, cell-line-specific, and perturbation-by-cell-line interaction components. Applied to four CRISPR-interference Perturb-seq screens on multiple cell lines, our framework reveals that these components have distinct structures and information requirements. The global response component is low-dimensional, reflects recurrent proliferation and stress response programs, and can be inferred from control gene expression. In contrast, the perturbation and cell-line specific components are high-dimensional and cannot be recovered from control expression. We therefore develop response-component-aligned models that map biological priors, such as gene coessentiality, onto the geometry of observed transcriptional responses. Critically, this alignment enables simple linear or multilayer perceptron (MLP) based models to outperform state-of-the-art architectures across multiple generalization settings, including unseen cell lines and combinations of unseen perturbations. Together, our framework for response decomposition and alignment provides a principled basis for evaluating and designing perturbation-prediction models, showing that generalization depends primarily on matching biological information to the response components rather than on model complexity alone.

bioinformatics↗

bioRxiv2026

Integrated Patient-Derived Xenograft and Patient-Derived Cell Models Reveal Therapeutic Vulnerabilities Beyond Standard-of-Care Therapy in Endometrial Cancer

Endometrial cancer (EC), the most common gynecologic malignancy in the USA, has seen limited improvement in patient outcomes over recent decades, underscoring the need for relevant preclinical models. To address EC heterogeneity, we established an integrated platform of patient-derived xenografts (PDXs) and matched patient-derived primary cancer cells (PDCs) for disease modeling and systematic drug sensitivity testing. Fresh tumor specimens (n=103) were collected from EC patients to generate PDXs in immunodeficient mice and corresponding PDCs. Fifty-three PDX models were successfully established (52% engraftment rate), with higher success observed in high-grade, recurrent, metastatic tumors (70%), compared with their low-grade counterparts (56%). Histopathologic and immunohistochemical analyses confirmed that PDX tumors faithfully preserved morphology, hormone receptor status, and intertumoral heterogeneity across multiple passages. Using 13 PDC models, we performed an unbiased screening of 179 FDA-approved oncology drugs, revealing marked intertumoral variability in drug response. Almost all PDC models exhibited limited sensitivity to NCCN-recommended therapies, highlighting the need for alternative treatment strategies. In contrast, multiple FDA-approved agents including epigenetic modulators, dual PI3-kinase/HDAC inhibitors, topoisomerase II inhibitors, and proteasome inhibitors demonstrated potent antitumor activity. Importantly, a low-dose combination of the DNA methyltransferase inhibitor 5-azacytidine and the histone deacetylase inhibitor romidepsin significantly suppressed tumor growth across six independent PDX models. Together, these findings establish a comprehensive PDX and PDC platform as a robust translational resource. By capturing the histopathologic and molecular diversity of EC and identifying clinically actionable therapeutic advantages, including an epigenetic combination regimen, this study offers a translational resource for preclinical drug evaluation.

cancer biology↗

bioRxiv2026

Imaging-Based Age- and Sex-specific Cardiovascular and Skeletal Phenotypes in Fbn1C1041G/+ Mice

Marfan syndrome is a multisystem connective tissue disorder with age-dependent and sex-dependent phenotypic variability. This study characterized early cardiovascular, valvular, transmitral flow, and skeletal changes in Fbn1C1041G/+ mice. Male and female wild-type and Fbn1C1041G/+ mice were examined from 4 to 20 weeks of age. Transthoracic echocardiography was used to measure aortic root and ascending aortic diameters, anterior mitral leaflet length, and mitral inflow Doppler parameters. Lateral X-ray imaging was used to quantify kyphosis angle. Fbn1C1041G/+ mice of both sexes developed progressive aortic dilation, with earlier and broader aortic root involvement in males and delayed annular dilation in females. Anterior mitral leaflet elongation was detected from 8 weeks in males and at 20 weeks in females. In contrast, reduced E-wave velocity and E/A ratio were present from 4 weeks in both sexes, without changes in A-wave velocity. Kyphosis was detectable earlier in females than in males. These findings show that early Fbn1-related phenotypes follow organ-specific and sex-dependent temporal patterns, supporting age-resolved and sex-stratified assessment in preclinical Marfan syndrome studies.

pathology↗

bioRxiv2026

Hyaluronan and CD44 targeting reverses early matrix changes, proinflammatory signals and fibrosis in primary sclerosing cholangitis

Primary sclerosing cholangitis (PSC) is a rare, progressive liver disease characterized by biliary inflammation and bile duct strictures and no approved medical therapy. Despite its clinical severity, the pathological mechanisms underlying PSC remain poorly understood, largely due to early diagnostic challenges. Here we provide complementary evidence in human PSC samples, transcriptomic data, mouse models, and 3D cholangiocyte cultures that underscore the importance of hyaluronic acid (HA) and its cognate receptor CD44 in PSC pathogenesis. HA is a glycosaminoglycan abundant in the extracellular matrix in inflammatory disorders, yet its role in PSC has not been well characterized. We demonstrate that in early-stage PSC, cholangiocytes aberrantly produce high molecular weight HA that accumulates in the peribiliary matrix, increasing local tissue stiffness. This mechanical signal is transduced by a CD44/Integrin {beta}1 receptor complex in cholangiocytes, driving cell proliferation, YAP mechanosignaling, pro-inflammatory cytokine production with a transition to a ductular reactive phenotype. CD44 knockdown in cholangiocyte cell lines and mouse models significantly lowered stiffness, and attenuated inflammation. Together, these findings reveal a mechano-inflammatory axis in which HA-driven matrix stiffening perpetuates biliary inflammation and disease progression, identifying HA targeting and CD44 as promising therapeutic strategies. One Sentence SummaryHyaluronan and CD44 mediate matrix changes and progressive fibrosis in primary sclerosing cholangitis.

pathology↗

bioRxiv2026

Haplotype-based insights into the genetic architecture of net blotch resistance in barley

Net blotch, caused by Pyrenophora teres, is a major constraint to barley production worldwide and occurs as two epidemiologically distinct forms: net form net blotch (NFNB) and spot form net blotch (SFNB). Although numerous resistance loci have been reported in recent years, their genetic relationship remains poorly understood, and the effective deployment of resistance is constrained by the complex genetic architecture of net blotch resistance. In this study, we used a haplotype-based mapping approach to dissect the genetic basis of resistance to NFNB and SFNB in a diverse panel of 950 barley accessions from the Australian Grains Genebank (AGG). Disease responses were evaluated across 13 experiments, and a total of 40 quantitative trait loci (QTL) were identified, including 26 associated with NFNB, 29 with SFNB, and 15 common for both diseases. Most loci co-localized with previously reported QTL, while six putative novel haploblocks highlighted untapped genetic diversity within the AGG collection. Correlation analyses across phenotypic, genetic and haploblock levels revealed a partial but incomplete overlap in resistance mechanisms between NFNB and SFNB. Among the 4,497 haploblocks, approximately 60% of them showed positive local genetic correlations between the two diseases, suggesting shared genomic contributions to resistance. Haplotype composition analysis further identified a resistant haplotype group, mainly comprising accessions of Asian origin, that exhibited high levels of resistance to both forms of net blotch. Through in silico haplotype stacking, we demonstrated the cumulative genetic potential achievable by combining favourable haplotypes. When the breeding objective was to improve resistance to both NFNB and SFNB, dual-disease stacking strategies outperformed single-disease approaches, highlighting the value of prioritising haplotypes with positive pleiotropic effects. Overall, this study provides a comprehensive haplotype-level framework for understanding net blotch resistance and delivers practical insights for breeding barley cultivars with durable and broad-spectrum resistance to both NFNB and SFNB.

plant biology↗

bioRxiv2026

A dual-layer computational framework for prioritising therapeutic candidates targeting extracellular vesicle-mediated immune escape in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy characterised by a highly immunosuppressive tumour microenvironment and limited therapeutic responses. Tumour-derived extracellular vesicles (EVs) contribute to PDAC progression by transferring immunomodulatory molecules and tumour-associated signals, suggesting EV-associated processes as potential intervention opportunities. However, the heterogeneity of EV biology and the complexity of tumour-immune interactions make single-target intervention strategies challenging. Here, we developed a computation-driven dual-layer candidate-prioritisation framework to identify potential modulators associated with PDAC EV-mediated immune escape through complementary production-side and action-side strategies. For the production-side layer, we focused on upstream processes related to EV biogenesis, cargo regulation, inflammatory signalling, and tumour-associated pathways. An 88-gene PDAC EV-associated target framework was integrated with cell-type-resolved prognosis annotations from ctPANDA and predicted targets of 18 natural products derived from Scutellaria baicalensis, Epimedium spp., and Cornus officinalis to prioritise natural-product candidates with disease relevance and potential chemical tractability. In parallel, key targets with experimentally resolved ligand-binding structures were subjected to pocket-guided de novo small-molecule design based on co-crystal ligand-defined binding sites, followed by structural, docking-based, and physicochemical screening of generated compounds. For the action-side layer, VHH and scFv binders were computationally designed and screened against extracellular regions of MET and CD81 to prioritise candidates potentially suitable for EV recognition and capture. This study provides a computational strategy for narrowing candidate spaces across both EV-associated production pathways and released vesicle recognition. The resulting small molecules, antibody-like binder models, and screening workflows provide a resource for future experimental validation of strategies targeting PDAC EV-associated immune regulation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/740294v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@11829b0org.highwire.dtl.DTLVardef@158efb5org.highwire.dtl.DTLVardef@1e17cc5org.highwire.dtl.DTLVardef@c69696_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Lineage-specific expansion of a potential novel class of resistance genes in Myrtaceae

Genes encoding intracellular nucleotide-binding site leucine-rich repeat (NBS-LRR) receptors represent the largest class of resistance (R) genes in plants, yet their evolutionary trajectory in trees remains poorly understood. Using high-quality long-read genome assemblies from eight Myrtaceae species, we identified 15,792 NBS-encoding genes with threefold variation in gene content across species. To investigate potential decoy domains for effector proteins of pathogens, we parsed the annotated NBS-encoding genes and determined 181 unique non-canonical domains. Notably, we observed frequent integration of Jacalin domains into TIR-NBS proteins. This novel gene family, named TNJ, is hypothesized to represent a new R gene class. Further exploration of TNJ sequence analysis shows up to seven Jacalin domains per protein and forming a monophyletic clade; however, AF3 modelling confirmed only six domains. Conserved residues in the TIR domain and functional motifs within the NB-ARC domain supports TNJs potential role in immune signalling. Most hypervariable sites and positively selected sites detected to be surface-exposed were clustered in the Jacalin region of TNJ, suggesting that surfaces of Jacalin domain may harbour residues determining pathogen recognition specificity. These findings support TNJ as a potentially new class of R genes in Myrtaceae with Jacalin as a replacement for LRR.

evolutionary biology↗

bioRxiv2026

Dronedarone hydrochloride reverses obesity-related metabolic syndrome while preserving skeletal muscle mass

Obesity-driven metabolic syndrome poses a critical global threat, yet standard therapies like GLP-1 receptor agonists trigger substantial lean mass wasting, with muscle loss accounting for up to 40% of reduced weight. Here we identify a non-canonical metabolic application for dronedarone hydrochloride, an anti-arrhythmic benzofuran derivative. In diet-induced and ob/ob obese mice, short-term dronedarone hydrochloride administration dose-dependently reduces food intake, clears visceral and subcutaneous adiposity, and reverses steatohepatitis. Head-to-head trials show that dronedarone hydrochloride achieves glycemic control and fat clearance non-inferior to semaglutide, tirzepatide, and empagliflozin, but uniquely and completely preserves skeletal muscle mass. Mechanistically, dronedarone hydrochloride operates independently of central hypothalamic appetite-regulating neuropeptides and the peripheral leptin pathway. By decoupling fat reduction from sarcopenia, our findings establish dronedarone hydrochloride as a muscle-sparing therapeutic candidate for metabolic syndrome.

pharmacology and toxicology↗

bioRxiv2026

Sequence-based modeling of plant epigenomes reveals cell-type-specific cis-regulatory grammar

How cis-regulatory sequences and their genetic variation govern chromatin accessibility and gene expression to establish plant cell identities remains incompletely understood, despite their fundamental roles in development, environmental responses, and phenotypic diversity. Here we present PEAgent, a framework for training, evaluating and interpreting deep-learning models that predict single-cell chromatin accessibility directly from DNA sequence, packaged in an interactive web portal and toolkit. Models were trained on single-cell chromatin-accessibility atlases of soybean, maize and rice, together spanning over 355,000 cells and 320 cell types and [~]150 million years of evolution. We unraveled a lexicon of 243 cell-type-resolved regulatory patterns, half of them composite, with TCP and bHLH showing the greatest influence and strongest conservation across species. Co-occurrence and in silico synergy analyses, explicitly modeling motif orientation and spacing, revealed two distinct cooperative modes acting at short and nucleosome-scale distances. We further showed that model predictions distinguish grass-conserved from rice-specific regulatory sequences far more accurately than sequence conservation scores alone, and validated the models predicted variant effects against cell-type-level chromatin accessible QTLs. PEAgent provides a foundational resource for decoding cell-type-specific plant cis-regulatory logic and interpreting noncoding variation in plants. HighlightsO_LIPEAgent predicts single-cell chromatin accessibility directly from DNA sequence in soybean, rice and maize. C_LIO_LINearly half of cell-type-resolved patterns are composite, with TCP and bHLH motifs most influential and conserved across species. C_LIO_LICo-occurrence and synergy analysis reveals distinct cooperative grammar at short and nucleosome-scale distances. C_LIO_LIPEAgent distinguishes grass-conserved from lineage-specific regulatory sequences better than sequence conservation scores alone. C_LI

genetics↗

bioRxiv2026

scWeave: A deep learning model that bidirectionally translates between gene expression and chromatin structure at single cell resolution

Chromatin structure and gene expression are intimately linked, yet characterizing how the two covary has proven challenging, primarily because the two modalities are rarely measured in the same cells. Recently, single-cell co-assay protocols have enabled simultaneous profiling of both modalities within the same cells, but these experiments remain costly and technically challenging. To better characterize the relationship between 3D chromatin architecture and gene expression and to enable cross-modality inference from single-modality measurements, we developed a model called scWeave that bidirectionally translates between gene expression (scRNA-seq) and 3D chromatin architecture (scHi-C) at single-cell resolution. The scWeave model employs dual autoencoders to extract separate cell-level latent representations and learns to translate between these representations using dedicated translation modules. We evaluate scWeave on six publicly available co-assay datasets spanning mouse embryonic development, mouse cortex, mouse olfactory epithelium, and human bone marrow. On held-out mouse cells, scWeave outperforms a nearest-neighbor baseline and existing methods adapted to single-cell resolution, achieving a 57% improvement in median Spearman correlation when predicting gene expression from chromatin structure and an 18.8% improvement in median HiCRep similarity in the reverse direction relative to the next-best baseline. We further show that scWeave learns cross-modally aligned latent representations at single-cell resolution, enabling cells profiled in one modality to be matched to their counterparts in the other. Finally, scWeave generalizes to entirely held-out developmental timepoints in mouse olfactory epithelium and performs well on held-out human bone marrow cells despite limited human training data. By predicting the unmeasured chromatin architecture or transcriptional state from a single measured modality, scWeave offers a route to extend the benefits of costly co-assays to the many cell types, developmental stages, and species that are currently profiled with only one modality.

genomics↗

bioRxiv2026

Pannexin 1 phosphorylation sites differentially modulate channel activity and physiological outcomes

Within the vasculature, pannexin 1 (PANX1) channels in smooth muscle cells (SMCs) regulate -adrenergic constriction and blood pressure. PANX1 channel activity is regulated by phosphorylation at Y198, S205 and Y308 residues, but the physiological significance of these modifications is unknown. Here, we utilize newly developed PANX1 Y198F, S205A and Y308F phospho-dead mutant mice to test physiological changes related to hemodynamics. Radiotelemetry-measured blood pressure was decreased in Y198F, increased in Y308F, but unchanged in S205A mice at baseline. Clonidine-sensitive sympathetic-driven hypertension was observed in all mouse lines except Y198F. Pressure myography of third-order mesenteric arteries revealed -adrenergic contractile responses were decreased in Y198F, slightly enhanced in Y308F, but unchanged in S205A, with responses in Y198F vessels mimicking controls treated with PANX1 inhibitors. To understand signaling changes driving these phenotypes, we performed mesenteric artery bulk RNA sequencing, but found a minimal number of differentially expressed genes between phospho-dead mutants and controls. Similarly, co-immunoprecipitation-mass spectrometry of wildtype or phospho-dead mutant-expressing vascular SMCs revealed few interacting proteins distinct to each PANX1 variant. However, PANX1 channel activity assessments in HEK293T cells expressing the 1D-adrenergic receptor as well as each phospho-dead mutant PANX1 showed that phenylephrine-induced ATP release from Y198F channels was significantly decreased compared to wildtype, but current was unaffected. Conversely, basal and phenylephrine-induced S205A and Y308F currents were reduced, but ATP release resembled controls. Taken together, these findings indicate that distinct PANX1 phosphorylation determines PANX1 metabolite release versus current conducting properties and in turn, regulates physiological outcomes in the vasculature. One Sentence SummaryPANX1 Y198 phosphorylation-mediated ATP release is a major driver of -adrenergic vasoconstriction in vascular smooth muscle cells.

physiology↗

bioRxiv2026

The secreted elastase SjCE2b drives host skin penetration by Schistosoma japonicum

Cercarial elastase is the most abundant protease secreted by Schistosoma mansoni and plays a critical role in cercarial invasion. Although Schistosoma japonicum encodes only a single elastase, SjCE2b, its secretion by cercariae and its specific function in skin penetration have remained elusive. Here, we report the first proteomic analysis of S. japonicum cercarial excretory-secretory products (ESPs) induced by linoleic acid or mouse skin, confirming the presence of SjCE2b in both ESPs preparations. Recombinant SjCE2b expressed in Pichia pastoris was characterized as a trypsin-like serine protease whose activity is entirely abolished by the elastase inhibitor MeoSuc-AAPF-CMK. Furthermore, SjCE2b expression was detected exclusively in cercarial extracts and localized specifically to the cercarial acetabular glands and ducts. Subsequent proteomic analysis indicates that SjCE2b can degrade numerous human epidermal proteins, including ten isoforms of type I and type II keratins. In vitro digestion assays further demonstrated that SjCE2b can digest key structural components of the dermis, including elastin, collogen, and fibronectin. Additionally, the cleavage of complement component C3 and immunoglobulins (IgA and IgG) suggests that SjCE2b may facilitate immune evasion by newly transformed schistosomula. Critically, the incubation of cercariae with anti-rSjCE2b antibody reduced the worm burden by 80.85%, confirming the essential role of SjCE2b in the skin penetration of S. japonicum cercariae and highlighting it as a compelling candidate for vaccine or therapeutic development. Author SummarySchistosomiasis constitutes a major global health burden caused by parasitic flatworms of the genus Schistosoma. Proteolytic and histolytic enzymes secreted by cercarial pre- and post-acetabular glands facilitate disruption of the host skin barrier and protect the parasite from localized dermal inflammatory response. Although cercarial elastase is a well-characterized invasion enzyme in Schistosoma mansoni, its role in Schistosoma japonicum remains poorly defined; consequently, S. japonicum cercariae have been hypothesized to rely on distinct repertoire of proteolytic enzymes during skin penetration. In the present study, we showed that SjCE2b was localized to the cercarial acetabular glands and ducts, and was secreted upon stimulation with linoleic acid or mouse skin. Functionally, SjCE2b can disrupt host skin integrity by degrading epidermal and dermal components, and may promote immune evasion through cleavage of complement component and immunoglobins. Furthermore, the antibody-mediated neutralization of secreted SjCE2b significantly impaired parasite penetration by greater than 80%. Together, these findings establish SjCE2b as a critical enzyme required for S. japonicum cercariae invasion and highlight its potential as a promising target for novel therapeutic interventions.

microbiology↗

bioRxiv2026

Teneurins Are SPARCL1 Receptors

Extensive experiments document that SPARCL1, a secreted protein that is produced primarily by astrocytes in brain and endothelia throughout the body and that is also known as Hevin, enhances synapse formation. However, the mode of action of SPARCL1 at synapses remains unclear owing to divergent results in the literature. Here, we use cultured neurons from newborn male and female mouse embryos to show that the C-terminal follistatin-like and Ca2+-binding domains of SPARCL1, which account for only 35% of the total SPARCL1 sequence, are sufficient to potently enhance synapse numbers. SPARCL1 acts at nanomolar concentrations at which SPARCL1 does not robustly bind to neurexins, neuroligins or neurexin/neuroligin complexes but avidly interacts with all teneurins. Strikingly, the follistatin-like domain of SPARCL1 on its own strongly binds to teneurins but is unable to stimulate synapse formation. Only when combined with the SPARCL1 Ca2+- binding domain does the follistatin-like domain induce synapses, suggesting that SPARCL1 enhances synapse numbers by binding to teneurins via its C-terminal follistatin-like domain and by activating synapse formation via its Ca2+-binding domain. SIGNIFICANCE STATEMENTSPARCL1 (also known as Hevin) is a synaptogenic factor that is produced primarily by astrocytes in brain, and that enhances synapse formation. How SPARCL1 acts at synapses, however, remains unclear because divergent results describe its binding partners at synapses and the sequences involved in its synaptogenic activity remain unclear. In the present study, we show that SPARCL1 avidly binds to the presynaptic teneurins adhesion molecules, that this binding is mediated by its small follistatin-like domain, and that its synaptogenic activity requires both its follistatin-like and its Ca2+-binding EC domains. Thus, our results suggest that SPARCL1 is recruited to developing synapses by binding of its follistatin-like domain to teneurins and then induces synapse assembly via its Ca2+-binding domain.

neuroscience↗

bioRxiv2026

IL-21-producing peripheral helper T cells associate with autoimmune bile duct injury in biliary atresia

BackgroundBiliary atresia (BA) is a severe neonatal liver disease characterized by progressive fibrosis and bile duct obliteration. ObjectiveAlthough immune dysregulation is implicated in the pathogenesis of BA, the specific mechanisms driving bile duct injury remain incompletely understood. This study aimed to characterize tertiary lymphoid structures (TLSs) within extrahepatic biliary remnants (EBRs), identify their cellular mediators, and evaluate the therapeutic potential of targeting IL-21 receptor signaling. DesignWe performed integrated bulk RNA sequencing, single-cell RNA sequencing, spatial transcriptomics, multiplex immunohistochemistry, and flow cytometry on clinical samples from BA patients and non-BA cholestatic controls. TLS maturation was assessed by CD23 immunohistochemistry in EBRs from 148 BA patients and correlated with clinical parameters. Anti-IL-21R antibody treatment was evaluated in a rhesus rotavirus-induced BA mouse model, with treatment initiated on day 4 post-infection. ResultsTLSs were identified in BA EBRs with significantly higher prevalence than in matched liver tissues. Mature TLSs containing CD23 germinal centers were associated with elevated serum matrix metalloproteinase-7, more advanced hepatic fibrosis, and localized autoantibody deposition on injured bile ducts. Single-cell profiling revealed expanded CD4+ T peripheral helper (Tph) cells expressing IL-21 and CXCL13 within TLS-containing EBRs. Tph cells were enriched in peripheral blood of BA patients compared to non-BA cholestatic controls (P = 0.0025), and serum IL-21 was significantly elevated (P < 0.0001). Post-infection IL-21R blockade in the mouse model reduced jaundice incidence, improved weight gain, prevented extrahepatic biliary obstruction, and significantly improved long-term survival. ConclusionTLSs in BA extrahepatic biliary remnants harbor expanded Tph cells associated with IL-21-mediated B cell activation and bile duct injury. IL-21R blockade ameliorated disease in a murine BA model, identifying the IL-21/IL-21R axis as a potential therapeutic target warranting further investigation. Key MessagesO_ST_ABSWhat is already known on this topicC_ST_ABSImmune dysregulation contributes to biliary atresia (BA), with documented lymphocyte infiltration and defective B cell tolerance. However, the cellular mechanisms linking local immune activation to bile duct injury are unclear, and the roles of organized lymphoid structures and specific CD4 T cell subsets in orchestrating local humoral responses have not been characterized. What this study addsThis study demonstrates that mature tertiary lymphoid structures in extrahepatic biliary remnants are associated with disease severity markers and localized bile duct injury in BA. We identify T peripheral helper cells as an expanded IL-21-producing CD4 T cell population within these structures, and show that post-infection IL-21 receptor blockade prevents biliary obstruction and improves survival in a murine BA model. How this study might affect research, practice or policyThese findings identify the IL-21/IL-21R signaling axis as a candidate therapeutic target in BA warranting further preclinical and translational investigation. TLS maturation status in biliary remnants and serum autoantibody levels may serve as potential biomarkers of disease severity, meriting prospective evaluation in clinical cohorts.

immunology↗

bioRxiv2026

Prior Context Scaffolds Sentential Semantic Integration during Noisy Speech Comprehension

Understanding speech in noise is a central challenge of everyday communication, yet listeners often succeed by using prior context. How the brain uses such context remains debated: it may refine predictions about upcoming words, or it may provide a higher-level framework that helps degraded speech cohere into meaning. Here we combined simultaneous EEG-fNIRS recording with hierarchical multivariate encoding models to track how prior context shapes speech processing from acoustics to words and sentential meaning. Participants listened to natural spoken narratives under clear speech, noisy speech, and context-supported noisy speech conditions. Context brought comprehension of noisy speech close to clear-speech levels. EEG revealed that contextual support reduced neural encoding of lexical surprisal and entropy, indicating weaker tracking of local word-level prediction demands. In contrast, when context was available, fNIRS showed enhanced encoding of sentence-level semantic integration across frontal regions and the right angular gyrus, and stronger angular gyrus encoding predicted better comprehension. By combining EEG and fNIRS to capture complementary electrophysiological and hemodynamic signals, this multimodal approach reveals a hierarchical shift in degraded speech comprehension: prior context does not simply improve word-by-word prediction, but scaffolds the integration of noisy input into coherent discourse.

neuroscience↗

bioRxiv2026

Group size and activity influence shoal choice in Goldfish: Replication of zebrafish findings using a drift-diffusion model

Animals often rely on social information when making movement decisions. In zebrafish, classic work showed that shoal size and shoal activity both bias shoal choice. Here we extend these effects in Goldfish (Carassius auratus) and extend them with a drift-diffusion model (DDM) account of individual evidence accumulation under dynamic social cues. Using a three-chamber linear arena, we quantified a focal fishs position for 10 minutes while manipulating (i) numerical differences between flanking shoals and (ii) their activity (swimming speed) via temperature manipulation. ANOVA on time-proportion choices confirmed robust attraction to larger shoals; when shoal sizes were equal, the more active shoal was preferred. In combined manipulations, activity effects dominated at small numbers but saturated as group size increased, indicating a threshold-like integration where activity dominates at small shoal sizes (<3 fish) but saturates at larger sizes. We formalize these processes with a bounded DDM in which a sigmoidal stimulus function maps shoal size and average speed to momentary evidence, subject to random perturbations. The model reproduces the observed psychometric relations between relative numerosity, velocity differences, and choice. Our results (i) generalize zebrafish findings to a carp species with distinct ecology and physiology, and (ii) provide a compact mechanistic link between social cues and individual decision trajectories in dynamic social contexts.

animal behavior and cognition↗

bioRxiv2026

Spatial Glyco-Codes Define Human Liver Pathology and Progression

Glycosylation is a fundamental process regulating cellular function, tissue organization, and disease progression. However, comprehensive glycan profiling at single-cell spatial resolution remains largely inaccessible, particularly in clinical archival tissues. Here we develop spatial-GPT, a multimodal platform for simultaneous profiling of glycans, proteins, and/or transcripts in archival formalin-fixed paraffin-embedded (FFPE) tissues. Using a panel of 30 DNA-encoded lectins recognizing major mammalian glycan motifs and structural classes, sequencing-based spatial-GPT (DBiT-GPT) mapped the spatial glycome, proteome, and transcriptome across 16 human liver specimens encompassing steatosis, fibrosis, cirrhosis, and hepatocellular carcinoma (HCC), leading to identification of spatial glyco-codes - combinatorial glycan states associated with distinct cellular identities, tissue features, and pathological processes. Unexpectedly, glyco-codes alone were sufficient to resolve major cell types, disease states, and HCC subtypes, revealing a previously unappreciated level of biological information encoded within the tissue glycome. Spatial glycomics uncovered tumor-like glyco-codes in premalignant regions, suggesting that glycan reprogramming may precede overt malignant transformation. Using imaging-based single-cell spatial glycan-protein profiling (CODEX-GP), we track glyco-codes across the whole-tissue architecture of 3 representative HCC samples. We further examined the glyco-codes across more than 300 patient specimens and quantified cell-type- and disease-specific glyco-codes as well as glycan-defined immune-evasion, T-cell-exhaustion, and steato-fibrotic niches. Together, these findings establish spatial glyco-codes as a previously unrecognized layer of tissue organization that encodes cellular identity, tissue function, and disease progression. The ability of glyco-codes to distinguish major liver pathologies across independent patient cohorts further highlights their potential as a new class of molecular histopathology biomarkers.

pathology↗