Biology subjects

Lee, S.

Publications and source records attributed to Lee, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

TDKC (Target Distilled K-mer Classifier): Ultrafast and Memory-Efficient Sequence Classification for Target Pathogen Diagnostics

Metagenomic sequencing can identify pathogens from clinical samples without prior knowledge of the causative agent. Yet, as sequencing workflows scale to process thousands of multiplexed samples simultaneously, classifying these samples against massive reference databases creates a significant computational bottleneck. Furthermore, large-scale applications such as screening public sequence repositories remain computationally challenging. Existing metagenomic classifiers are designed for full-taxon classification, where the goal is to identify all organisms in a sample. However, many diagnostic applications focus on detecting a specific set of clinically relevant pathogens. This constraint can be exploited to significantly lower computational costs. Here we present TDKC (Target Distilled K-mer Classifier), a method for targeted metagenomic classification. TDKC constructs a compact index by distilling target-specific k-mers from a full-taxon reference database. When classifying clinical samples, TDKC uses 16.9-33.6x less memory and is 5.1-34.7x faster than per-read full-taxon and targeted classifiers (Kraken2, Centrifuger, CLARK), while maintaining high sensitivity and low false positive rates. Against the sketch-based profiler Sylph, TDKC remains 3.8x faster and uses 8.7x less memory. TDKC also supports per-k-mer accession tracking across over 3 million source accessions for downstream subtype analysis, and domain-level detection of bacteria, archaea, and viruses. By reducing the index to only the pathogens of interest, TDKC makes targeted pathogen detection feasible at scale.

bioinformatics↗

bioRxiv2026

PETase Kubu enables near-complete enzymatic depolymerization of commercial PLA/PBAT blend mulch film

Agricultural mulch films improve crop productivity, but post-use recovery and recycling remain difficult because the films are thin, fragmented, dispersed across fields, and contaminated. Commercial PLA/PBAT blends are increasingly used as biodegradable mulch film materials, yet these films exhibit slow or incomplete degradation under environmental conditions. Here, we show that Kubu, a thermostable PETase from Kutzneria buriramensis, rapidly depolymerizes commercial PLA/PBAT mulch film without pretreatment at 60 {degrees}C, achieving 95% mass loss within 96 h and releasing terephthalate, adipate, and lactate, detected by LC-MS/MS and HPLC, as the major monomeric products of both PBAT and PLA components. GPC and SEM revealed extensive degradation at the polymer-water interface. DiffDock docking against Kubu, IsPETase, and TfCut indicates that the canonical W/F(Y) cleft of the PETase/Cutinase fold accommodates aliphatic and aromatic ester bonds with comparable geometry, suggesting that substrate promiscuity is an inherent property of the cleft architecture. Kubus distinctive contribution combines this permissive cleft with catalytic activity sufficient for near-complete blend depolymerization within 24 h. Integration with a socioeconomic analysis shows that complete enzymatic depolymerization could avoid social costs up to $4,087 per ton of mulch film. These findings establish a single-enzyme approach to end-of-life management of heterogeneous polyester blends.

bioengineering↗

bioRxiv2026

Systematic Engineering of Intra-Articular Drug Release Profiles Reveals a Key Determinant of Disease-Modifying Efficacy in Post-Traumatic Osteoarthritis

Post-traumatic osteoarthritis (PTOA) is a progressive joint disease for which no disease-modifying osteoarthritis drugs (DMOADs) have been approved. Although injectable drug delivery systems can prolong therapeutic retention within the joint, it remains unclear whether local drug release kinetics influence disease-modifying efficacy. Here, we developed a modular platform of injectable supramolecular hydrogels using biocompatible, generally recognized as safe (GRAS) amphiphilic molecules and systematically engineered a range of degradation and drug release profiles. Using the cathepsin-K inhibitor L-006235 as a model DMOAD, we generated hydrogels with distinct release kinetics and evaluated their therapeutic performance in PTOA. Hydrogels exhibiting slower degradation and more sustained drug release like Sucrose Stearate (SS hydrogel) showed prolonged intra-articular retention and improved therapeutic outcomes. In a destabilization of the medial meniscus (DMM) mouse model, sustained-release formulations significantly reduced cartilage degeneration, preserved aggrecan expression, improved joint histopathology, and enabled effective monthly dosing. In contrast, formulations with faster degradation and release kinetics required more frequent administration to achieve comparable benefits. To our knowledge, this is the first study to establish local drug release kinetics as a critical determinant of disease-modifying efficacy in PTOA. This work provides one of the clearest demonstrations to date that engineering intra-articular release kinetics, rather than merely prolonging residence time, can improve disease-modifying outcomes. Our findings establish local release kinetics as a key design parameter for osteoarthritis therapeutics and highlight the potential of tunable supramolecular hydrogels for long-acting drug delivery.

bioengineering↗

bioRxiv2026

The small RNA Teg16 represses rsbV and modulates SigB-dependent gene expression in Staphylococcus aureus

Staphylococcus aureus relies on coordinated regulatory networks to adapt to environmental stress and host-associated conditions. The alternative sigma factor SigB plays a central role in this process and is controlled by the anti-anti-sigma factor RsbV, which functions as a key regulatory node in the pathway. While numerous small regulatory RNAs (sRNAs) have been identified in S. aureus, relatively few have been directly linked to the SigB stress response network. Here, we investigated the role of the small RNA Teg16 in post-transcriptional regulation of the SigB stress response pathway. Computational prediction identified a region of complementarity between Teg16 and the translational initiation region of rsbV. To test a potential regulatory effect based on this prediction, teg16 was overexpressed, and rsbV transcript levels were measured by quantitative RT-PCR. Teg16 overexpression resulted in reduced rsbV transcript levels and decreased expression of SigB-dependent genes, including asp23 and the carotenoid (crt) biosynthesis operon responsible for staphyloxanthin pigment production. In addition, strains carrying the teg16 expression construct exhibited altered hemolytic activity under the conditions tested, suggesting effects on virulence-associated phenotypes. We further examined whether Teg16 influences the global regulator CodY and observed reduced codY transcript levels at early time points following teg16 overexpression. Together, these results extend a previously identified regulatory relationship between Teg16 and CodY and raise the possibility of a feedback relationship linking post-transcriptional regulation to metabolic control. These findings identify Teg16 as a previously uncharacterized regulator that connects small RNA-mediated control to the SigB stress response network in S. aureus. ImportanceThe alternative sigma factor SigB is a central regulator of stress adaptation in Staphylococcus aureus and influences both metabolism and virulence-associated phenotypes. While numerous small regulatory RNAs (sRNAs) have been identified in this organism, few have been functionally linked to control of the SigB pathway. Here, we identify the small RNA Teg16 as a regulator of rsbV, a key modulator of SigB activity. Teg16-dependent repression of rsbV is associated with reduced expression of SigB-dependent genes and measurable changes in phenotype, including decreased pigment production and altered hemolytic activity. In addition, our findings extend a previously identified relationship between Teg16 and the global regulator CodY, suggesting integration of post-transcriptional regulation with metabolic control. These results establish Teg16 as a previously uncharacterized component of the SigB regulatory network and provide new insight into how small RNAs contribute to stress adaptation in S. aureus.

microbiology↗

bioRxiv2026

Ultrasensitive voltage imaging reveals distinct electrical microdomains in neurons

For the brain to compute, electrical signals must propagate over the membranes of individual neurons, connecting synaptic inputs to synaptic outputs1. Complex neuronal morphologies coupled with the spatial organization of synaptic inputs and outputs enable diverse voltage transformations that underlie cell-type specific computations2,3. However, measuring these transformations in vivo has remained challenging, leaving a crucial gap in our mechanistic understanding of single neuron computation. Here, we develop ASAP7y, a genetically encoded voltage indicator with unprecedented subthreshold sensitivity and expanded excitation compatibility in both mice and flies. We leveraged ASAP7y combined with two-photon random-access microscopy to record sensory stimulus-evoked voltage dynamics with millisecond, subcellular, and subthreshold resolution along the neurites of individual neurons in Drosophila. We found remarkable heterogeneity in voltage propagation across cell-types, delineating a fundamental axis of electrical diversity. Leveraging a nanoscale EM reconstruction of the visual system4, we modeled the electrotonic properties of single neurons spanning 717 cell types, revealing how morphology shapes voltage transformations. Finally, we demonstrate that confined voltage propagation creates substrates for local computation, producing subcellular domains with distinct feature selectivity across multiple cell types. These results provide mechanistic insight into how critical single neuron computations arise and reveal parallel processing in single neurons.

neuroscience↗

bioRxiv2026

Oral exposure to Perfluorooctanoic acid disrupts the microbiota-gut-liver axis and enhances the severity of chemically induced colitis in mice.

Inflammatory bowel diseases (IBD) affect millions of patients worldwide and impair quality of life. Although genetic and environmental factors are known to disrupt the gastrointestinal (GI) epithelial barrier and increase susceptibility to IBD, the precise contribution of specific environmental exposures remains unclear. Per- and polyfluoroalkyl substances (PFAS), or "forever chemicals," are widely used in consumer products and contaminate food and water sources, resulting in chronic oral exposure worldwide. Perfluorooctanoic acid (PFOA), a common PFAS, has been epidemiologically associated with the development of IBD, particularly in older adults. Here, we assessed the effects of oral PFOA exposure on the GI tract, liver, and susceptibility to colitis. C57BL/6 mice were exposed to PFOA (0.1 mg/kg or 1.0 mg/kg) beginning at weaning (post-natal day [P]21) for a time course of 4 or 8 weeks. GI physiology/pathology (Ussing chambers; histology), expression of pro-inflammatory cytokines (qPCR), microbiota composition (16S sequencing), bile acids production (qPCR; LC/MS), and liver pathology (histology) were assessed. Colitis susceptibility was evaluated in genetically predisposed (IL10 knockout) mice, and in induced (dextran sodium sulfate [DSS]) mouse models following PFOA exposure (8 weeks at 1.0 mg/kg). Oral PFOA exposure increased intestinal permeability, mildly increased cytokine expression, altered gut microbiota composition, disrupted liver and serum bile acids, and caused hepatic hypertrophy at higher doses and longer exposure. Although PFOA did not increase disease susceptibility in genetically predisposed Il10 KO mice, it significantly worsened DSS-induced colitis, but only in male mice. Together, these findings demonstrate that early-life PFOA exposure disrupts the gut-liver axis and may contribute to colitis development in a sex dependent manner.

pharmacology and toxicology↗

bioRxiv2026

Identification of Heterogeneous Cortical Thickness Patterns Associated with Prenatal Gestational Diabetes Exposure: A SuStaIn-Based Subtyping Study

ImportancePrenatal exposure to gestational diabetes mellitus (GDM) has been associated with adverse metabolic, neurodevelopmental, and psychiatric outcomes in offspring. However, whether GDM-exposed youth exhibit heterogeneous neuroanatomical patterns remains unclear. ObjectiveTo identify distinct cortical thickness subtypes among GDM-exposed youth and examine their associations with anthropometric, neurocognitive, psychiatric/behavioral and neuroimaging measures both cross-sectionally and longitudinally. Design, Setting, and ParticipantsThis cohort study used the Adolescent Brain Cognitive Development (ABCD)(R)data, a multisite longitudinal population study. Subtype and Stage Inference (SuStaIn), an unsupervised machine learning framework, was applied to cross-sectional structural MRI data to identify cortical thickness patterns in 573 GDM-exposed youth and 2854 healthy controls. Posthoc longitudinal analyses included 1,853 observations from a subset of GDM-exposed youth with 1-, 2-, and 4-year follow-up visits to examine subtype differences in developmental trajectories over time. Exposure(s)Prenatal exposure to GDM. Main Outcome(s) and Measure(s)The primary outcomes included identification of cortical thickness subtypes and their inferred regional ordering patterns. Secondary outcomes included subtype-specific anthropometric, neurocognitive, psychiatric/behavioral and neuroimaging measures. ResultsThe GDM-exposed sample had a mean age of 119.02 {+/-} 7.34 months and was 47.5% female. Two cortical thickness subtypes were identified. Between subtypes, Subtype 1 (63.2%) was characterized by earlier inferred insula involvement and was associated with greater height (d = 0.36, pFDR < 0.001) and weight (d = 0.26, pFDR = 0.007), whereas Subtype 2 exhibited earlier inferred frontal involvement and nominally higher Attention-Deficit/Hyperactivity Disorder (ADHD) prevalence (d = 0.08, p = 0.036), steeper longitudinal cortical thinning across all six cortical regions of interest ({beta} range: -0.05 to -0.13, all pFDR < 0.05), and a smaller decline in Obsessive-Compulsive Disorder (OCD) prevalence over time ({beta} = -1.02, pFDR = 0.049). Conclusions and RelevanceGDM exposure was associated with two distinct offspring cortical thickness subtypes, each showing different inferred regional ordering patterns and clinical associations. One subtype showed an insula-cingulate-predominant pattern associated with anthropometric measures, whereas the other showed a frontal-predominant pattern associated with nominally higher psychiatric measures and faster cortical thinning over time.

neuroscience↗

bioRxiv2026

Vagus nerve stimulation limits colonic inflammation through distinct neuroimmune circuitry shaped by inflammatory history

Bidirectional communication between the nervous and immune systems has been demonstrated to limit or enhance immune cell function across organ systems and conditions. Although these neuroimmune circuits can become activated as an anti-inflammatory reflex, vagus nerve stimulation (VNS) reduces inflammation in models of endotoxemia, rheumatoid arthritis, and intestinal inflammation. In the spleen during endotoxemia, VNS activates a "cholinergic anti-inflammatory pathway" (CAIP), whereby choline acetyltransferase (ChAT)-expressing T cells release acetylcholine to reduce macrophage activation. VNS can also drive CAIP-independent pathways to reduce inflammation in the spleen and intestinal tract, although the circuitry modulating colonic inflammation remains underexplored. Here, we demonstrate that left cervical VNS reduces acute LPS-induced inflammation, evidenced by reduced Tnfa expression in colon and spleen and decreased circulating TNF. In the colon, these protective effects required efferent but not afferent VNS and were independent of ChAT+ T cells, IL10, {beta}-adrenergic signaling, and colonic sympathetic innervation. Critically, the ability of VNS to modulate colonic inflammation depended on prior tissue-specific inflammation. Mice recovering from DSS colitis, despite near-complete histological recovery, were refractory to the protective effects of VNS in the colon. This lack of efficacy in the colon was not reflected in measures of inflammation in the spleen or serum, highlighting the need for target-organ-specific monitoring. This loss of efficacy after colonic inflammation was transient, with restoration occurring upon complete recovery. These findings demonstrate that VNS efficacy in colonic inflammation depends on circuitry distinct from canonical systemic anti-inflammatory pathways, and that tissue responsiveness is shaped by anatomical site and inflammatory history. Key PointsO_LIElectrical stimulation of the left cervical vagus nerve reduces LPS-induced inflammation in the mouse colon. C_LIO_LIThis colonic anti-inflammatory effect requires vagal efferents but not afferent signaling. C_LIO_LIUnlike canonical splenic anti-inflammatory pathways, the colonic response does not require ChAT+ T cells, IL-10, {beta}-adrenergic signaling, or local sympathetic innervation. C_LIO_LIRecent DSS colitis abolishes colonic responsiveness to VNS despite preserved splenic and systemic anti-inflammatory effects. C_LIO_LIRecovery of VNS anti-inflammatory efficacy after colitis shows that neuroimmune responsiveness in the colon is dynamically shaped by inflammatory history. C_LI

immunology↗

bioRxiv2026

CSF-Seq enables transcriptome-wide profiling of cerebrospinal fluid and identifies prognostic signature of leptomeningeal disease

Leptomeningeal disease (LMD) is a rapidly fatal complication of systemic cancer for which sensitive diagnostic tools and informative biomarkers remain limited. Here, we introduce CSF-Seq, a method for whole-transcriptome sequencing of cell-free RNA (cfRNA) from human cerebrospinal fluid (CSF), designed to enable molecular profiling of LMD and other central nervous system (CNS) conditions. Using a prospectively collected CSF biobank, we analyzed 125 samples spanning multiple pathologies, including breast and lung LMD, glioblastoma, traumatic brain injury, and non-cancer neurological controls. Through optimized RNA extraction, library preparation, and deep sequencing, CSF-Seq generated robust and reproducible transcriptome-wide profiles despite the low abundance and fragmentation of cfRNA in CSF. CSF transcriptomes exhibited disease-specific expression, separating LMD from non-cancer controls and from non-LMD cancers, independent of CSF collection modality. Tumor-associated epithelial transcripts, including CEACAM6 and MUC1, were consistently enriched in LMD samples, whereas immune and CNS-associated transcripts were broadly detected across disease states, consistent with contributions from both tumor and non-tumor sources. Cross-site processing of matched samples demonstrated high concordance, indicating preservation of sample-specific transcriptional signatures across independent workflows. Importantly, we identified a collection method- independent LMD gene expression signature that was significantly associated with overall survival, supporting its potential prognostic relevance. Together, these findings establish CSF-Seq as a technically robust and clinically informative platform for transcriptomic biomarker discovery in CNS metastatic disease, offering a minimally invasive approach for disease characterization, risk stratification, and longitudinal monitoring in patients with LMD.

cancer biology↗

bioRxiv2026

Evolutionary rate correlations reveal long-term co-evolutionary interactions in Drosophila melanogaster

Co-evolution between genes can occur for a variety of reasons, including co-expression of genes, epistatic interactions between them, physical interactions of gene products and many others. Co-evolutionary partners of a gene are therefore of great interest in identifying potential factors that contribute to any phenotype of interest. State-of-the-art approaches to detect these interactions use correlations of evolutionary rates across a broader phylogeny, and so by necessity identify interactions only among genes that are present across long evolutionary time periods. This makes the methods unwieldy when interest lies in a single focal organism in which the genes of interest may have evolved in the recent evolutionary past. Here, we present a new approach to calculating evolutionary rate correlations which focuses on extracting maximum coverage for a single focal species, while retaining signals of co-evolution across large clades. We show how this approach is able to identify potential interactions even in highly studied species and highly studied genes, with a focus on the D. melanogaster sex-determiner, Sxl, using data from 72 species of Dipterans.

evolutionary biology↗

bioRxiv2026

Spatiotemporal Dynamics of Highly Pathogenic Avian Influenza H5 Virus Introductions and Regional Spread in the Republic of Korea

Highly pathogenic avian influenza (HPAI) viruses from clade 2.3.4.4 have caused recurrent outbreaks in poultry since 2014. In the Republic of Korea, clade 2.3.4.4b viruses have driven five epidemic waves, yet the factors underlying HPAI introduction and farm-to-farm spread remain poorly understood. We compiled hemagglutinin gene sequences of clade 2.3.4.4b viruses from wild birds and poultry in the Republic of Korea (October 2016-March 2024) and reconstructed dispersal dynamics using Bayesian phylogeography. Dispersal patterns suggest that domestic duck farms in the western provinces likely form a key interface for spillover from wild birds into poultry. Mixed-effects generalized linear models showed that both wild-to-poultry and farm-to-farm transition rates were positively associated with the number of poultry farms in the destination province, while wild-to-poultry rates were further associated with higher avian influenza virus infection probability among wild birds. Wild-to-poultry transition rates were lower in 2020-2024 than in 2016-2018, which may reflect strengthened interventions. These findings suggest that poultry farm abundance and introduction pressure from wild birds jointly shape the spatial dynamics of HPAI introduction and spread. More broadly, these factors may provide operational indicators to guide risk-based surveillance and control strategies. Author SummaryHighly pathogenic avian influenza (HPAI) H5 viruses continue to cause major losses in poultry and pose recurring risks at the wildlife-livestock interface. Effective control depends on identifying where viruses are most likely to enter poultry populations and how they spread between farms. Using viral genomic data from wild birds and poultry in the Republic of Korea, this study suggests that domestic duck farms in western provinces likely form a key interface for introductions from wild birds into poultry. We also found that regions with more poultry farms were more likely to receive and spread the virus, while introduction risk was further elevated where infection pressure from wild birds was higher. By linking viral genomic patterns with ecological and epidemiological information, our study helps identify where HPAI viruses are most likely to enter poultry populations and spread between farms. These findings can guide targeted surveillance and early control in regions at greatest risk.

evolutionary biology↗

bioRxiv2026

Developmental plasticity of cancer-associated fibroblasts contributes to the malignant progression of gastric cancers

Cancer-associated fibroblasts are transcriptionally heterogeneous, yet how their reprogramming shapes gastric cancer progression remains unclear. Integrating single-cell and spatial transcriptomics, patient-derived fibroblast co-culture, and clinical cohorts, we identified a spatially organized continuum of extracellular matrix-producing fibroblasts. An inferred trajectory connected homeostatic ECMh through inflammatory-chemoattractive ECMi to tissue-remodeling ECMr, with increasing GLIS2 regulon activity and ECMr enrichment near the tumor-stroma interface. ECMr co-culture induced a non-EMT epithelial program characterized by coordinated laminin-332 subunit expression, hemidesmosome-associated genes, a matrix-remodeling protease profile, and reduced proliferative activity. Longitudinal imaging showed progressive cancer-cell elongation and positional displacement over the fibroblast layer. ECMr-associated GLIS2 regulon activity in resected primary tumors was associated with shorter peritoneal metastasis-free survival across two gastric cancer cohorts, with a similar association in colorectal cancer. A peritoneal metastasis recapitulated the corresponding stromal and epithelial organization. Together, these findings define an ECMr-centered stromal-epithelial wound-repair circuit linked to subsequent peritoneal dissemination.

cancer biology↗

bioRxiv2026

Regional reconfiguration of functional brain networks during childhood and adolescence: evaluating age and sex effect

IntroductionWhile global topological properties of brain networks reach relative maturity early in development, functional reconfigurations at the regional level continue throughout adolescence to support cognitive maturation. However, regional age and sex-specific developmental patterns of functional reconfiguration remain incompletely understood. MethodsWe analyzed resting-state fMRI data from 528 participants aged 5-21 years from the Human Connectome Project in Development. Three regional graph-theory metrics (betweenness centrality, hub score, and local efficiency) were computed for each individuals functional network. Cognition was measured using NIH toolbox. Parallel factor analysis was employed to decompose an individual x region x metric array into factors representing distinct developmental properties in the full sample and separately for males and females. Brain-cognition associations were examined in developmental subgroups (<13, 13-18, >18 years). ResultsThree factors emerged, characterizing visual, multimodal integration, and higher-order factors. Across development, metrics capturing network integration (betweenness centrality and hubness) showed general stability, while metrics capturing segregation (local efficiency) presented distinct peaks, particularly in the visual factor. Females showed earlier peaks and declines in higher-order factor, while males exhibited greater variability and protracted maturation in multimodal and higher-order factors. Brain-cognition associations were modest with early childhood and crystallized cognition composites showed small negative correlations with hub score in entire sample (r=-0.212) and local efficiency in males aged <13 years (r=-0.215). ConclusionFindings highlight nonlinear, sex-specific functional reconfiguration at region-level during childhood and adolescence, underscoring the importance of sex-stratified analyses in developmental and providing a crucial foundation for future investigations of developmental disorders.

neuroscience↗

bioRxiv2026

Ectopic hAMH-driven SOX17 expression induces hyperplastic Sertoli valve formation in mouse testes

In the terminal segment of the seminiferous tubules, SOX17 expression in the rete testis (RT) epithelium plays a crucial role in the formation of the Sertoli valve (SV), as revealed by phenotypic analyses of RT-specific Sox17 conditional knockout (cKO) mouse testes. In these RT-specific Sox17 cKO testes, SV disruption leads to the backflow of RT fluid into the seminiferous tubules, resulting in defective spermiogenesis and male infertility. Although valve deformation in the Sox17 cKO testes is likely caused indirectly by impaired downstream actions of Sox17 in the RT, the mechanisms by which SOX17 in RT influences SV formation in the seminiferous tubules remain unclear. To address this, we generated a novel AMH-Sox17 transgenic (Tg) mouse line carrying a human AMH promoter-driven Sox17 cDNA cassette. We analyzed the phenotypes of the Sertoli valve and spermatogenesis in AMH-Sox17 Tg mice, as well as in RT-specific Sox17 cKO; AMH-Sox17 Tg double mutant mice. Ectopic SOX17 (SOX17+) expression in Sertoli cells resulted in excessive Sertoli valve structures with acetylated tubulin bundles in the terminal segment of the AMH-Sox17 Tg testes, along with enhanced WNT4/RSPO1 signaling, suggesting the enhanced valve formation of ectopic SOX17+ Sertoli cells by themselves. Moreover, the AMH-Sox17 Tg could partially rescue the SV deformation and infertility in RT-specific Sox17 cKO mice, leading to proper SV formation, normal spermiogenesis and a partial recovery of male fertility in AMH-Sox17 Tg; RT-specific Sox17 cKO double mutant mice. These findings genetically demonstrate that ectopic SOX17+ Sertoli cells can compensate for SOX17 paracrine signaling in the RT, underscoring a key shared downstream pathway between RT and SV. Summary statementThe paracrine actions downstream of ectopic SOX17 expression in the Sertoli cells not only promote the valve formation, but also partially rescue the defective spermiogenesis of the rete testis-specific Sox17-null mice.

developmental biology↗

bioRxiv2026

Identifying Context-Specific Cell-Cell Interaction Genes Without Ligand-Receptor Databases from Spatial Transcriptomics

Current approaches to inferring cell-cell interactions (CCIs) are largely constrained by predefined ligand-receptor databases, particularly for low-resolution spatial transcriptomics (ST) platforms such as Visium. Due to the difficulties in accurately resolving interacting cells at coarse spatial resolution, other modes of interaction are often overlooked. Low-resolution ST data, however, can serve as an alternative to high-resolution ST, which suffers from low sensitivity, and to image-based ST, which is limited by restricted gene panels. Here, we present CellNeighborEX v2, a database-free framework that directly infers CCI-associated genes from ST data by detecting deviations between observed and expected gene expression at the spot-population level. These deviations are rigorously evaluated through a hybrid statistical framework involving permutation testing and are further refined by considering the abundance of interacting cell-type pairs. Compared with other conventional approaches relying on ligand-receptor databases, CellNeighborEX v2 can capture CCI genes from a broad spectrum of interactions, including both paracrine signaling and contact-dependent communication. Across datasets from hippocampus, liver cancer, colorectal cancer, ovarian cancer, and lymph node infection, CellNeighborEX v2 accurately recapitulated previously identified CCIs. Notably, it uniquely detected interactions absent from existing ligand-receptor databases, enabling detection of context-specific CCIs from Visium data. CellNeighborEX v2 is a tool that expands the analytical spectrum of Visium data and deepens our understanding of the molecular language of intercellular communication.

bioinformatics↗

bioRxiv2026

Label-free quantitative 3D mapping of collagen architecture by holotomography

Fibrillar collagen architecture regulates tissue mechanics and cell-matrix interactions, but following how collagen-rich matrices assemble and remodel in three dimensions requires non-destructive measurements that can link structure to matrix-associated mass without exogenous labels. Here we present holotomography (HT) as a label-free platform for volumetric imaging and quantitative profiling of reconstituted fibrillar collagen. Volumetric RI tomograms resolved fibrillar collagen networks without exogenous labels, and co-registration with second-harmonic generation (SHG) microscopy supported the correspondence between HT-resolved RI structures and SHG-positive fibrillar collagen. Curvelet-transform-based segmentation of representative axial sections converted the tomograms into fiber-level descriptors, including morphology, orientation and RI-derived fiber-associated dry mass. At the matched 0.8 mg/mL condition, HT resolved distinct network organization, with type I forming thicker, more sparsely distributed fibers and type III a finer, denser network, while mean fiber-associated RI remained comparable between subtypes. Across the concentration series, type I showed stronger increases in fiber width and RI-derived mass, whereas type III remained comparatively fine. Time-lapse HT further captured RI dynamics during type I fibrillogenesis and visualized local cell-matrix reorganization in HT1080 cell-embedded gels, capturing cells and surrounding matrix in a single label-free measurement. Together, these results position HT as a complementary label-free approach for volumetric visualization and RI-based quantification of collagen-rich extracellular matrices.

cell biology↗

bioRxiv2026

Millisecond nonlinear state changes during droplet coalescence identify therapeutic-antibody developability liabilities

Apoha's Liquid State Machine records ellipsometric waveforms from injections depositing sub-microgram quantities of antibody drop-by-drop onto a liquid reservoir. We previously showed that a behavioural feature extracted from the waveforms, VIBE1, identified antibodies carrying multiple biophysical liabilities in an industrial dataset of 71 monoclonal antibodies, and enriched for clinical failure across a larger dataset of 235 therapeutic antibodies. Here, we use an auxiliary coalescence-sensor channel to decode VIBE1 by separating the coalescence event from its propagation through the substrate. The per-titration drop-to-drop standard deviation of pinch-off time, {sigma}{tau}, explains most of VIBE1's variance across the dataset (R2 = 0.92, n = 1182). High-speed imaging at 10,000 frames per second reveals that all imaged drops initially thin at the same Newtonian capillary-inertial rate while the neck remains wide. In drops from certain antibodies, the thinning bridge then decelerates as internal strain builds in the narrowing neck. This elastocapillary stiffening response has a timescale {lambda} that decreases as pinch-off time {tau}i increases across the imaged set. {sigma}{tau} is therefore a readout of the antibody's propensity to undergo a transient gel-like stiffening response during coalescence, and that variability is what VIBE1 captures. The signal is concentration dependent, and absent in bovine serum albumin (BSA) tested at up to an order of magnitude higher concentration than the antibodies, despite BSA being a strongly surface-active globular protein. The instrument is configured so that complex behaviours of this kind appear in its recorded waveforms; the gel-like coalescence response we identify here is one such phenomenon.

biophysics↗

bioRxiv2026

Stress-Responsive Protein IFRD1 Protects Assembled Ribosomes via a Ribosome-Salvaging Mechanism

The ability of epithelial cells to cope with injury and undergo regeneration depends on tightly coordinated cellular responses. IFRD1 is a stress-responsive protein that is evolutionarily conserved and required for the cellular regeneration program paligenosis; however, how IFRD1 works in paligenosis is not known. Here we demonstrate that IFRD1 is primarily a cytosolic ribosome-binding protein, specifically binding 80S monosomes that are not actively engaged in translation. Using multiple in vivo and in vitro injury models, including cerulein-induced pancreatitis in mice and tunicamycin-induced ER stress in cell culture, we demonstrate that IFRD1 acts as a ribosome-salvaging factor, preventing ribosomes from degradation. In the absence of IFRD1 during ER stress, non-translating 80S ribosomes were unstable and prone to disassembly and selective degradation. The resulting accumulation of degraded ribosomal subunits overwhelmed cellular autophagic machinery, as evidenced by accumulation of the autophagy-tagging protein p62, even though overall autophagic flux remained unaffected. Ultimately, cells lacking IFRD1 showed reduced mTORC1 activity followed by increased cell death, consistent with patterns observed in cells lacking IFRD1 during paligenosis. Thus, we detail a previously unrecognized cellular function for IFRD1 in stabilizing and preserving the mature ribosome pool during metabolic and translational transitions such as paligenosis.

cell biology↗