Biology subjects

Lin, X.

Publications and source records attributed to Lin, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Ventricular Expansion Couples Hyperosmotic Stress to Thirst

Thirst is thought to arise from osmotic signals detected by circumventricular organs, yet how hyperosmotic stress activates mechanosensitive channels remains unclear because cell shrinkage should reduce membrane tension. Here we identify a brain-scale mechanical signal that couples systemic osmotic stress to drinking. In mice, hypertonic saline rapidly increased serum and cerebrospinal fluid osmolality, expanded the lateral ventricles, and promoted water intake. Relieving or blocking ventricular deformation attenuated drinking without eliminating osmotic gradients. Hyperosmotic challenge also produced localized deformation of periventricular cells, where spatial transcriptomics revealed candidate mechanosensitive channels, including Tmem63b and Piezo1. Thus, ventricular expansion provides a mechanical component of osmotic thirst, uncovering an osmo-mechanical layer of interoceptive regulation.

neuroscience↗

bioRxiv2026

Galectin-8 Modulates Membrane CD44v Localization and Tempers STAT3 Signaling in Gastric Metaplasia

ABSTACTGalectin-8 is a lectin that binds N-acetyllactosamine moieties with preference towards those with acidic, terminal modifications (-O-sialyated, 3-O-sulfated). As CD44-variants (CD44v) are biomarkers of metaplasia and cancer, a hyaluronic acid receptor that modulates STAT3 signaling, and specifically expresses 3-Sialyl-LeA/X glycotopes, we asked whether galectin-8 might play a role in gastric metaplasia. Using a synchronous, chemically induced murine model that produces gastric spasmolytic polypeptide expressing metaplasia (SPEM), we compared Lgals8-/- mice to congenic wild-type C57BL/6J mice. We found that galectin-8 was necessary for membrane localization of CD44v on SPEM cells at the base of the glands, suggesting a physical interaction between galectin-8 and CD44v. Metaplastic glands from Lgals8-/- mice had an increase in nuclear pSTAT3 compared to C57BL/6J mice, suggesting that galectin-8 restrains CD44 -> STAT3 signaling. This effect was more prominent in the neck compared to the base, which has greater abundance of CD44v after injury in Lgals8-/- mice. Derepression of STAT3 signaling may explain why low galectin-8 levels is associated with a worse prognosis in gastric cancer.

cancer biology↗

bioRxiv2026

Galectin-3 is Necessary for Selective Cathartocytosis, which Expedites the Development of Proliferative Gastric SPEM

The expression and secretion of sulfated colonic-type mucins is a feature of high-risk metaplasias of the gastrointestinal foregut (Barretts esophagus, type III intestinal metaplasia of the stomach, and pancreatic intraepithelial neoplasia). Galectin-3 is a lectin that preferentially associates with galactose modified by a 3-O-sulfate relative to its unmodified counterparts and is upregulated as the tissue transitions to high-risk metaplasia, dysplasia, and cancer. Since both galectin-3 and sulfated glycotopes are aberrantly and concurrently overexpressed in high-risk premalignant and malignant tissue transformations, we sought to investigate the role of galectin-3 in the metaplastic reaction. We found that injury induces the expression of Lgals3 at the RNA and protein levels. Unlike cancer cell lines, we show that in vivo galectin-3 colocalized with sulfomucins in zymogenic granules of the gastric chief cell. Utilizing a synchronous, chemically-induced murine model that produces spasmolytic polypeptide expressing metaplasia, we found that galectin-3 facilitates cathartocytosis of the vesicles it resides in, but not organelles lacking LGALS3. Inhibition of cellular downscaling resulted in delayed expression of the metaplastic transcription factor Sox9 as well as proliferation. Here, we present a new role for galectin-3 in promoting the transition from normal, homeostatic tissue to metaplasia and our data suggest that cathartocytosis represents an unconventional secretory pathway for galectin-3, which has been a matter of controversy as galectins are not secreted via canonical pathways.

cancer biology↗

bioRxiv2026

R-loop Prediction Reveals Generalization Limits of DNA Foundation Models Beyond Regulatory Genomics

DNA foundation models are increasingly proposed as general-purpose representations for genomic prediction and design, yet their evaluation remains largely centered on conventional regulatory tasks. This leaves a critical question unresolved: do DNA foundation models generalize to sequence biology beyond conventional gene regulation? To answer this question, we introduce RloopBench, a systematic benchmark for R-loop-forming sequence prediction as a biophysically distinct, genome-stability-associated task. We compare rule-based methods, task-specific models, classical sequence encodings, and foundation model representations across in-distribution, cross-platform, consensus-level, and cross-species evaluations. Foundation models achieve strong performance when positive and negative sequences are compositionally separable, but this advantage does not consistently transfer to cross-platform and cross-species settings, where they are often comparable to classical k-mer representations. Unexpectedly, a one-hot classifier baseline shows the strongest overall sensitivity to R-loop-forming sequences, exceeding more complex models across several generalization tests. Rule-based and task-specific models also exhibit limited transfer outside their original training regimes. Performance is further shaped by sequence properties, negative-control design, experimental platform, and species-specific genomic context. Together, RloopBench establishes genome-stability-associated sequence prediction as a complementary direction for DNA foundation model development and evaluation, while underscoring that simple sequence encodings remain necessary baselines for assessing model generalization beyond conventional regulatory tasks.

bioinformatics↗

bioRxiv2026

Decoding Immune Reconstitution Failure in People Living with HIV through Single-cell Genomics

Immune non-responders (INRs), a subset of people living with HIV (PLWH), fail to achieve full immune reconstitution and remain at increased risk of morbidity, mortality, and non-AIDS-related illnesses. As the mechanisms underlying this impaired immune recovery remain poorly understood, we performed single-cell multi-omics profiling on peripheral blood mononuclear cells from 43 INRs, 47 immune responders and 53 healthy donors. Our dataset comprises 2,744,009 transcriptomes and 1,226,658 chromatin-accessibility profiles across 58 identified immune cell types. INRs exhibited markedly elevated inflammatory signaling, increased apoptotic activity, and dysregulation of immune-activating ligand-receptor interactions. Additionally, we identified 2,996 interaction cis-eGenes and 5,938 cis-caPeaks, and validated key cell type-specific cis-xQTL effects associated with immune reconstitution failure. Furthermore, we identified 3,551 sc-eQTLs and 872 cell-state interaction eQTLs (ieQTLs) in CD4+ T cells. A genotype-specific upregulation of OAS3 in INRs, likely regulated by STAT1, was identified based on these results. We developed scPRISM (single cell Predictive Reconstitution Immune Status Model), a multi-modal framework that integrates scRNA-seq and scATAC-seq data to perform the dual tasks of differentiating disease states and predicting gene expression from chromatin accessibility, thereby deciphering the cell type-specific cis-regulatory basis of the disease. Our study delineates the transcriptional and epigenomic landscape of immune dysregulation in INRs and provides new genetic insights into HIV-associated immune reconstitution failure. These findings offer a foundation for developing biomarkers and precision therapies to restore immune function in PLWH.

genetics↗

bioRxiv2026

Transmembrane Domain Dominance Drives Emergent Signaling and Allosteric Inversion in mGlu1/5 Heterodimers

Class C GPCRs function as obligate dimers in which only one G protein can engage the complex at a time, but how each protomer contributes to heterodimer coupling has remained unresolved. Using CODA-RET, a BRET-based assay reporting direct Gq recruitment to defined, full-length receptor pairs, we show that signaling at the mGlu/ heterodimer flows predominantly through the mGlu protomer; domain-swapped chimeras localize this dominance to the transmembrane domain. The dominance generates emergent signaling: cis-acting mGlu PAMs and NAMs undergo allosteric inversion when coupling is restricted to mGlu. By contrast, the mGlu-selective NAM MTEP is silent at the heterodimer, mirroring mGlus minimal role in driving Gq. Because the mGlu PAM tested acts only in cis, a trans-acting mGlu PAM would theoretically be selective for mGlu/ homomers. These findings open a pharmacological design space in which protomer target and cis-versus-trans mode of action tune selectivity across mGlu/, mGlu/, and mGlu/ dimers.

neuroscience↗

bioRxiv2026

Neuromodulation of Foxp2+ hypothalamic neurons induces therapeutic hypothermia

The inability to selectively trigger therapeutic hypothermia independent of environmental cooling has hindered causal analysis of its broader physiological benefits. Here, we employed P57, a natural product that pharmacologically induces therapeutic hypothermia circumventing external cold stress, to identify the neuronal substrates underlying hypothermia-induced antitumor effects. Integrating functional ultrasound imaging, activity-dependent neuronal labeling, and single-nucleus RNA sequencing, we identify a previously unrecognized population of Foxp2 neurons in the medial preoptic area (MPA) that are selectively activated by P57. Inhibition of MPA Foxp2+ neurons abolishes P57-induced hypothermia, whereas the paraventricular hypothalamus (PVH) serves as a critical downstream node. Importantly, targeted activation of MPA Foxp2 neurons is sufficient to induce sustained hypothermia, suppress systemic metabolism, and inhibit tumor growth, providing causal evidence that neuronally driven reductions in core body temperature can exert antitumor effects. Together, these findings establish MPA Foxp2 neurons as a controllable node for therapeutic hypothermia induction and demonstrate that neuromodulation of defined neuronal populations can achieve therapeutic benefit by directly controlling physiological states.

neuroscience↗

bioRxiv2026

EnzCast: Prediction of Patient-Specific Enzymatic Kinetics through Multi-Modal Deep Learning and Isoform-Resolved Bayesian Inference based on Single-Cell Transcriptomics

Enzyme kinetic parameters underpin mechanistic biology but remain sparse in physiological context. We present EnzCast, a multi-modal framework jointly predicting Km, kcat, kcat/Km, and Ki from protein sequence, 3D structure, substrate chemistry, and experimental conditions, paired with IsoKin, an isoform-resolved Bayesian framework converting EnzCast priors into patient-specific in vivo kinetics. Trained on KinBench, the largest curated kinetics database, task-adaptive EnzCast achieved R2 = 0.413, 0.455, 0.227, and 0.105 for Km, Ki, kcat, and kcat/Km, surpassing all baselines on catalytic tasks. Systematic condition scans recovered compartment-specific pH direction inversion and pathway-level temperature responses. In a 20-patient colorectal cancer single-cell cohort, IsoKin reduced posterior uncertainty by 73.3% and 77.3%, revealing cell-type-specific rewiring. Orthogonal validation--scFEA flux, DepMap essentiality (permutation P = 0.0008) and TCGA survival-- provided mixed but directionally consistent support. Together, EnzCast and IsoKin bridge in vitro prediction, condition-aware biochemical interrogation and patient-resolved in vivo inference.

bioinformatics↗

bioRxiv2026

Predictive pursuit emerges in high-dimensional recurrent neural networks

Tracking dynamic moving objects in the external world is ethologically important for many organisms. Recent experiments have examined neural dynamics supporting such behaviors by employing visually-guided pursuit in freely moving rodents, yet computational principles underlying this cognitive process are not well understood. To address this, we developed a recurrent neural network model for examining the predictive behaviors and computations that emerge during pursuit. We demonstrate that the model generates internal predictions of the targets future locations, with anticipatory behaviors increasing with exposure to stereotyped trajectories of the target. These internal predictions can be used by the model to pursue a target in a complex environment, and the models emergent strategy is aligned with behavior when tested in rodents. In investigating the computations that underlie the models ability to perform predictive pursuit, we found units sensitive to the position of the target relative to the artificial agent, a representation analogous to egocentric target neurons observed in animals performing pursuit tasks. Ablating these units significantly reduced model performance, establishing a causal role of this functional response type in efficient pursuit. Given the complexity of the task and agent behavior, we hypothesized that RNN models may use high-dimensional neural codes to support predictive pursuit. To test this, we trained models of varying rank and found that anticipatory behavior emerged only when the rank was sufficiently high, despite strong pursuit performance in lower rank models. All RNNs encoded the egocentric location of the target, whereas allocentric self and target locations emerged only in high-dimensional networks. Overall, our results suggest that, unlike commonly studied vision, motor, or memory tasks, predictive pursuit emerges in high-dimensional networks with sufficient resources.

neuroscience↗

bioRxiv2026

Geometry-enhanced protein language modeling enables discovery of novel antibiotic resistance genes

The global antibiotic resistome remains largely unexplored, not because antibiotic resistance genes (ARGs) are rare in the environment, but because many are evolutionarily distant from known ARGs. Current computational approaches primarily rely on sequence homology, and thus miss distant homologues. We develop GeoARG, a geometry-enhanced framework that integrates structural features with protein language models through knowledge distillation, enabling efficient large-scale screening using sequence input alone. Across multiple benchmarks, GeoARG substantially improves the detection of remotely homologous ARGs, particularly under low sequence identity and fragmented conditions. Large-scale metagenomic analysis uncovers 1,485 high-confidence ARG candidates that are highly divergent from known ARGs, expanding the phylogenetic and functional landscape of the resistome. Structural analyses further show that these candidates preserve active-site geometry and maintain stable ligand-binding configurations consistent with known resistance mechanisms. These results demonstrate that geometric constraints enable systematic expansion of the resistome and facilitate the discovery of evolutionarily distant yet functionally conserved genes. A public web server is available at https://ycclab.cuhk.edu.cn/GeoARG/.

bioinformatics↗

bioRxiv2026

Mouse models with human antibody repertoires for inducing multiple lineages of HIV-1 broadly neutralizing antibodies

The complementarity determining region (CDR) 1, 2 and 3 of antibodies are the principal antigen contact sites. The heavy chain CDR3 (CDR H3) is highly variable, because it includes random nucleotide additions by the terminal deoxynucleotidyl transferase (TdT). Some broadly neutralizing antibodies (bnAbs) against the human immunodeficiency virus-1 (HIV-1) rely heavily on CDR H3 to recognize conserved epitopes on HIV-1 Envelope (Env) protein. Elicitation of comparable bnAbs is a prime goal of HIV-1 vaccine development, but the shortage of precursor antibodies with suitable CDR H3s in human repertoire is a major challenge for immunogen design. To aid this effort, we generated six mouse models for inducing bnAbs against major HIV-1 Env epitopes. In each mouse model, the immunoglobulin heavy and light chain loci were engineered to predominantly rearrange the germline V, D and J segments of a bnAb lineage. Owing to CDR3 diversity, only a small subset of the V(D)J recombination products may encode variable regions that can engage bnAb epitopes with sufficient affinity to initiate immune response. Therefore, these mouse models can be used to test and optimize immunization strategies to induce bnAbs from rare and diverse precursors in complex antibody repertoires.

immunology↗

bioRxiv2026

A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development

Lung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datasets, genetically engineered mouse models, human and murine LUSC cell lines, and multi-omics analyses, we demonstrate that SMAD4 deficiency promotes LUSC progression by unleashing EP300-mediated enhancer-promoter looping at the SOX2 locus. Mechanistically, SMAD4 does not directly bind SOX2 regulatory elements but instead constrains chromatin looping by sequestering EP300 away from loop anchor regions. Loss of SMAD4 leads to enhanced H3K27ac deposition, aberrant SOX2 activation, and increased LUSC tumor cell proliferation. Together, these findings reveal a non-canonical role for a transcription factor (e.g., SMAD4) in regulating dysregulated 3D genome architecture to inhibit tumor development.

cancer biology↗

bioRxiv2026

An oxytocin-gated circuit from the hypothalamus silences olfactory tubercle neurons to drive prosocial grooming

Spontaneous helping behaviors such as allogrooming are vital for survival in social species, yet their underlying neural mechanisms remain largely unknown. Although oxytocin (OXT) is known to modulate allogrooming, the precise neural circuits, molecular pathways, and sensory drivers remain unclear. Here, using a social emergency paradigm in mice, we show that observer mice selectively allogroom distressed, anesthetized conspecifics, a behavior that is guided by main olfactory system cues and mitigates the demonstrators anxiety. We identify an oxytocinergic circuit from the paraventricular hypothalamus to the medial olfactory tubercle (PVNOXT[->]mOT) that is necessary and sufficient for this helping behavior. In vivo fiber photometry reveals that PVNOXT[->]mOT activity and OXT release are temporally locked to allogrooming initiation. This behavioral effect requires oxytocin receptor (OXTR) signaling specifically on mOT dopamine D1 receptor-expressing neurons, where OXTRs suppress neuronal excitability via G protein-gated inwardly rectifying K+ (GIRK) channels. Disruption of this inhibitory mechanism induces neuronal hyperexcitability and impairs allogrooming, a deficit rescued by restoring GIRK function. These findings define a PVNOXT-mOT circuit for prosocial helping, revealing an oxytocinergic pathway with potential therapeutic relevance for neuropsychiatric disorders characterized by social deficits.

neuroscience↗

bioRxiv2026

Three immunoregulatory signatures define non-productive HIV infection in CD4+ T memory stem cells

The persistent HIV reservoir constitutes the main obstacle to curing HIV/AIDS disease. Our understanding of how non-productive HIV infections are established in primary human CD4+ T cells during the first round of infection remains, however, incomplete. In this study, we leveraged the HIV reporter virus pMorpheus-V5 to delineate cellular expression patterns that are upregulated in non-productively infected primary CD4+ T memory stem cells (TSCM). We found that CD4+ TSCM harboring non-productive proviruses displayed a distinct transcriptomic signature comprising 118 upregulated genes. This non-productive expression profile was distinct from that of productively infected cells as well as from negative-exposed and mock-infected cells. Among the cellular genes most upregulated in CD4+ T cells harboring non-productive proviruses were CCR4-binding migratory chemokines (CCL22, CCL17), tryptophan catabolic enzymes (IDO1, KYNU), and genes encoding cytoskeletal rearrangement proteins (BASP1, TNFAIP2). Intracellular flow cytometry-based analyses confirmed that non-productively infected CD4+ TSCM cells were enriched for CCL22 and IDO1 co-expression compared to the other CD4+ memory subsets, underscoring a clear CD4+ T cell subset specificity for the upregulation of these two immune gene sets associated with non-productive infections. These findings suggest that primary human CD4+ TSCM harboring non-productive proviruses display a distinct immunoregulatory phenotype which may facilitate immune evasion and contribute to the persistence of the HIV reservoir.

microbiology↗

bioRxiv2026

Metabolic adaptation to maternal hyperglycemia via ACLY-dependent acetyl-CoA production drives epigenetic remodeling and dysregulated placental development

AbstractsGestational diabetes mellitus (GDM) is a common metabolic complication of pregnancy that is paradoxically associated with both fetal overgrowth and fetal growth restriction (FGR). While maternal hyperglycemia is widely presumed to drive macrosomia through excessive nutrient supply, the mechanisms underlying FGR remain poorly understood. Here, using a mouse model that recapitulates the small-for-gestational-age (SGA) phenotype observed in human GDM pregnancies, we identify placental underdevelopment as a principal driver of FGR. Despite systemic nutrient abundance, hyperglycemic placentas exhibit reduced mass and an increased fetal-to-placental weight ratio, indicative of placental insufficiency. Mechanistically, maternal hyperglycemia induces anabolic metabolic rewiring while suppressing oxidative phosphorylation (OXPHOS), accompanied by upregulation and nuclear redistribution of ATP-citrate lyase (ACLY). ACLY converts glucose-derived carbon into acetyl-CoA in the cytosol and nucleus, thereby coupling glycolytic flux to lipid and hexosamine biosynthesis as well as to global histone hyperacetylation. This hyperacetylation-associated epigenetic reprogramming activates metabolic, innate immune, and inflammatory gene programs while repressing pro-proliferative and anti-apoptotic pathways. Consequently, placental growth is compromised despite nutrient excess. Importantly, activation of the ACLY-acetyl-CoA axis and global histone hyperacetylation is consistently observed in human GDM placentas across diverse birth outcomes, suggesting a conserved metabolic-epigenetic adaptation to maternal hyperglycemia. Together, these findings identify ACLY-dependent acetyl-CoA production as a central metabolic node linking maternal hyperglycemia to chromatin remodeling and placental development control, thereby reshaping fetal growth trajectories.

developmental biology↗

bioRxiv2026

PARG inhibition sequesters nuclear PAR-binding proteins, including XRCC1 and its partners, into nuclear condensates to elicit cytotoxicity

DNA breaks activate PARP1/2 to synthesize poly(ADP-ribose) (PAR), which relaxes chromatin and recruits DNA repair factors. Normally, PAR is short-lived, rapidly degraded by poly(ADP-ribose) glycohydrolase (PARG). While PARP1/2 inhibitors are established therapies for homologous recombination (HR)-deficient cancers, predictive biomarkers for PARG inhibition (PARGi) remain undefined. Using parallel genome-wide CRISPR screens with PARP and PARG inhibitors, we show that PARGi is synthetically lethal with loss of several PAR-binding factors, including XRCC1-LIG3, POLB, ALC1/CHD1L, ARH3, and PARG itself, but notably not with HR deficiency. Conversely, loss of PARP1, NMNAT1 (required for nuclear NAD synthesis), or UNG (upstream of APE1 cleavage and PARP1 activation), confers PARGi resistance. Mechanistically, PARGi induces time- and dose-dependent formation of PARP1-and PAR-dependent nuclear condensates containing XRCC1 and associated repair factors in otherwise undamaged cells. These condensates do not harbor active DNA breaks but instead sequester PAR-binding repair proteins, depleting their available nuclear pool and impairing their recruitment to genuine DNA breaks. While our analysis focused on XRCC1, PARG inhibition likely sequesters additional PAR- and PARP1-binding proteins. Thus, we propose that PARGi sequesters PAR-binding proteins to elicit toxicity, explaining the essentiality of PARG (but not PARP1) and identifying the loss of PAR-binding factors as candidate predictive biomarkers for PARG-targeted therapy.

molecular biology↗

bioRxiv2026

Neurocognitive deficits in controlling aversive memory among insomnia disorders

BackgroundInsomnia disorder is a common sleep disturbance characterized by adverse daytime cognitive and emotional impairments, such as repetitive negative thinking and increased psychological distress. Memory control, a key self-regulatory ability to control or inhibit unwanted thoughts and memories, plays an essential role in supporting cognitive functions and emotional well-being. Here, we delineate the neurocognitive mechanisms underlying memory control among individuals with insomnia. Methods41 participants meeting DSM-5 criteria for insomnia disorder and 40 healthy sleepers completed an emotional Think/No-Think task, during which participants either retrieved (Think) or suppressed the retrieval (No-Think) of aversive memories in response to memory cues while electroencephalograms were recorded. ResultsLinear mixed model analyses with age and depression scores as covariates showed that participants with insomnia exhibited impaired memory control abilities, as evidenced by reduced suppression-induced forgetting in memory recall when compared to healthy sleepers. Electrophysiologically, healthy sleepers showed enhanced right prefrontal theta power in retrieval suppression than in retrieval, indicating elevated needs of inhibitory control during memory control. In sharp contrast, this difference was absent among those with insomnia. Notably, the greater the severity of insomnia symptoms, the smaller the retrieval vs. retrieval suppression theta power differences across participants, linking inefficient top-down control of unwanted memories with low sleep qualities. ConclusionIndividuals with insomnia showed impaired memory control of aversive memories and aberrant electrophysiological activities during retrieval suppression. Future research shall investigate the causal relationship between memory control abilities and insomnia symptoms.

neuroscience↗

bioRxiv2026

Enteric sensory neurons for nutrient detection and gut motility

The enteric nervous system (ENS) orchestrates gastrointestinal reflexes and brain-gut communication via molecularly diverse neurons. Among these, intrinsic primary afferent neurons (IPANs) are essential for detecting luminal nutrients and irritants, yet their molecular identities, sensory properties, and functions remain poorly resolved. Here, we establish a segment-resolved single-cell atlas of the murine ENS, including a comprehensive characterization of the gastric ENS. This resource defines a refined taxonomy of enteric neurons and glia and enabled the development of a genetic toolkit for molecularly defined IPANs. Using chemogenetics and calcium imaging, we discovered that myenteric neurons detect a wide range of nutrients, irritants, and cytokines. Nutrient detection depends on a functional connection between chemosensory epithelial cells and enteric neurons mediated by 5-HT--HTR3 axis. Through optogenetic analysis, we demonstrated segment-specific regulation of gut motility by different IPANs. Our work establishes a genetic and physiological framework for enteric-specific sensory mechanisms.

neuroscience↗