Biology subjects

Liu, J.

Publications and source records attributed to Liu, J..

At least 181 records · Page 10Linked to original sources

bioRxiv2026

Intestinal Dysbiosis in Necrotic Enteritis: Dissecting the Roles of Eimeria and Clostridium perfringens

Necrotic enteritis (NE), caused by Clostridium perfringens, is a major enteric disease in poultry with substantial economic impact. NE is frequently triggered by co-infection with Eimeria spp., yet the relative contributions of Eimeria and C. perfringens to NE-induced dysbiosis and disease progression remain poorly defined. To address this, Cobb broiler chickens were challenged with Eimeria maxima, C. perfringens, or both, and ileal and cecal microbiota were analyzed using 16S rRNA gene sequencing and shotgun metagenomics. Temporal dynamics of intestinal microbiota shifts were further assessed at multiple time points post-infection. Our findings demonstrate that NE-associated dysbiosis is characterized by enrichment of pathobionts including C. perfringens, Escherichia, and Enterococcus cecorum, along with differential abundance of certain lactic acid-and short chain fatty acid-producing bacteria. Dysbiosis and disease progression were driven by synergistic interactions between E. maxima and C. perfringens, with E. maxima exerting a dominant influence. Notably, E. maxima alone promoted expansion of commensal C. perfringens or closely-related bacteria, even without prior exposure. Metagenomic analysis of the cecal microbiota further revealed a functional shift favoring utilization of host-derived glycans and simple carbohydrates over dietary fibers, in response to E. maxima and NE challenges. This transition coincided with E. maxima-induced epithelial damage, increased mucogenesis, and nutrient malabsorption. NE-associated dysbiosis emerged four days post-E. maxima infection and peaked 2-3 days following C. perfringens challenge. These findings suggest that Eimeria infection creates a permissive intestinal environment for C. perfringens colonization and proliferation, underscoring its pivotal role in NE pathogenesis. IMPORTANCENE is a major health and economic burden in poultry production, primarily driven by C. perfringens and potentiated by Eimeria infection. This study provides critical mechanistic insights into the distinct and synergistic roles of E. maxima and C. perfringens in NE disease progression. We show that Eimeria plays a dominant role in driving NE-associated dysbiosis and disease progression by inducing epithelial damage, inflammation, and nutrient malabsorption, which facilitate C. perfringens colonization, proliferation, and toxin production. Comprehensive characterizations of both structural and functional microbiome shifts revealed that NE-associated dysbiosis is marked by enrichment of facultative pathobionts that favors utilization of host-derived mucins and simple dietary carbohydrates, alongside depletion of strictly anaerobic, fiber-fermenting, SCFA-producing bacteria. These microbial shifts reflect disease progression and offer potential biomarkers for early diagnosis and therapeutic intervention. Our findings lay a foundation for microbiota-based diagnostics and interventions to mitigate NE and other enteric diseases.

systems biology↗

bioRxiv2026

FlcE latches onto the FliL-stator complex to turbocharge flagellar motility in Borrelia burgdorferi

Periplasmic flagella are essential for the distinctive morphology and motility of the Lyme disease spirochete Borrelia burgdorferi, and motility plays a critical role in its pathogenic lifestyle. These flagella are powered by specialized motors that contain a large spirochete-specific multiprotein collar complex, yet the molecular architecture and mechanisms underlying high-torque motility remain poorly understood. Here, we identify the tetratricopeptide repeat (TPR)-containing protein BB0298 as a previously unrecognized flagellar collar component and rename it FlcE. Loss of flcE results in altered morphology and nearly abolishes the spirochetes motility. Using cryo-electron tomography and biochemical analyses, we show that FlcE occupies a unique position within the collar where it surrounds the FliL-stator complex by binding to FliL and the collar protein FlcA. These findings support a model in which FlcE functions as a molecular "latch" that secures stator assemblies to sustain efficient torque generation. Notably, flcE is conserved across most motile members of the Spirochaetales and is located within the division and cell-wall (dcw) gene cluster. More broadly, the conservation of TPR-containing structural proteins across diverse bacterial flagellar systems suggests a general architectural principle whereby dedicated scaffolds reinforce stator complexes to maximize motor performance under high mechanical loads. ImportanceSpirochetal motility requires the stable engagement of torque-generating stator units, yet the mechanisms that secure these complexes have remained unknown. Here, we identify FlcE as a previously unrecognized collar protein that functions as a molecular latch by restraining the FliL-stator complex. Loss of FlcE destabilizes FliL-stator assemblies and severely impairs motility, demonstrating that peripheral scaffolding is essential for sustaining high torque output in the Lyme disease spirochete Borrelia burgdorferi. The conservation of tetratricopeptide repeat domains in FlcE and other bacterial flagellar proteins further suggests a broader mechanism in which specialized scaffolds anchor and stabilize stator complexes, enabling high torque generation. Because motility is a central virulence determinant in many pathogenic bacteria--including B. burgdorferi during transmission from the tick to the mammalian host and subsequent infection--defining the mechanistic role of FlcE provides important insight into the molecular basis of motility-driven pathogenesis and suggests new strategies for disrupting bacterial infection.

microbiology↗

bioRxiv2026

Molecular grammar of RNA m6A modification in ribonucleoprotein granules

Diverse RNA chemical modifications collectively regulate nearly all aspects of RNA metabolism. Among these, N6-methyladenosine (m6A) is the most prevalent internal modification in eukaryotic messenger RNAs. Recent studies have implicated m6A in the formation and regulation of ribonucleoprotein (RNP) granules--biomolecular condensates that organize RNA metabolism in space and time. However, the underlying biophysical mechanisms remain to be elucidated. Here, building on SMART, a single-molecule platform for quantitatively measuring RNP granule assembly across nanometer-to-mesoscale regimes, we develop SMART-epi to enable precise control of the m6A modification ratio. Using this approach, we show that physiological m6A levels inhibit YTHDF2 RNP granule assembly while directing specific RNA-RNA interaction architectures. Moreover, YTHDF1/2/3 exhibit distinct assembly kinetics, suggesting functional divergence. Together, these findings reveal a molecular grammar by which m6A modulates condensate dynamics and suggest that RNA modifications can encode regulatory information to tune RNP granule behavior, with potential implications for therapeutic intervention.

biophysics↗

bioRxiv2026

Chemogenetic Inhibition of Lateral Hypothalamus Inputs to the Paraventricular Thalamus Reduces Goal-Tracking in a Behaviorally Flexible Subgroup of Male Rats

The paraventricular nucleus of the thalamus (PVT) has emerged as an important node in circuits regulating motivated behavior. The neuronal pathway from the lateral hypothalamus (LH) to the PVT has specifically been shown to regulate arousal, feeding, and reward seeking. However, the involvement of the LH-PVT pathway in individual differences in cue-motivated behavior remains unclear. During a Pavlovian conditioned approach paradigm, when a reward is repeatedly preceded by the presentation of a cue, rats come to exhibit a conditioned response to the cue. One extreme of the population, sign-trackers (STs), approach and interact with the cue itself; while the other extreme, goal-trackers (GTs), approach the location of reward delivery. Intermediate responders (IRs) approach and interact with both the cue and reward location, without a clear preference. We utilized a Pavlovian conditioned approach paradigm to examine the effects of LH-PVT pathway inhibition on individual differences in cue-motivated behavior. A dual-vector approach was used to selectively express inhibitory chemogenetic receptors in the LH-PVT pathway. We found that inhibition of the LH-PVT pathway selectively attenuates the expression of goal-tracking behavior, without affecting sign-tracking. This effect is driven primarily by IR rats, as inhibition of LH-PVT neurons attenuates goal-tracking behavior in IRs, without impacting the response of STs or GTs. We speculate that the flexibility of responding in IR rats made them especially vulnerable to this manipulation. These findings identify the LH-PVT pathway as a selective contributor to reward-directed conditioned responding and a circuit substrate for behavioral flexibility. Significance StatementIndividuals differ in how reward-predictive cues motivate behavior, a feature linked to vulnerability and resilience to maladaptive reward seeking. The paraventricular thalamus (PVT), a midline hub with broad limbic connectivity, and its input from the lateral hypothalamus (LH) influences arousal, feeding, and reward seeking, but the role of the LH-PVT pathway in individual variability in cue-motivated behavior is unclear. We used chemogenetics to selectively suppress LH-PVT neurons during a Pavlovian conditioned approach paradigm. Inhibiting this projection reduced goal-tracking without altering sign-tracking, and this effect was driven primarily by intermediate responders, a phenotype characterized by behavioral flexibility. These results implicate LH-PVT signaling in reward-directed conditioned responding and suggest that this pathway contributes to flexible cue-motivated behavior.

neuroscience↗

bioRxiv2026

Machine Learning Assisted Optimization Framework for Designing Transcranial Focused Ultrasound Phased Array Transducer for Deep Brain Neuromodulation in Mice

Transcranial focused ultrasound is an emerging noninvasive neuromodulation technique offering high spatial precision and deep penetration. However, in deep brain neuromodulation in mice, the skull base attenuates the signal, distorting the focal region and creating off-target peaks. This study presents a machine-learning-driven simulation framework to optimize a bowl-shaped phased-array transducer design for hypothalamic targeting and compares its performance with that of time-reversal phase conjugation and a single-element baseline. A computed tomography-based mouse head model was used for full-wave acoustic simulations with a fixed bowl geometry (10 mm aperture, 6 mm radius of curvature). Designs were evaluated across various parameters, including operating frequency (0.2-1.5 MHz), active element count (16, 32, 64, 128), and element diameter (300-550 m). The evaluation employed four metrics: the presence of a -3 dB focal region within the hypothalamic area, axial focal length defined by the -3 dB full-width at half maximum, focal fragmentation measured by the -3 dB blob count, and targeting displacement. Random Forest surrogate models were trained in simulation outputs and paired with the Non-dominated Sorting Genetic Algorithm II to reduce computational costs during multi-objective optimization. The forward-excitation-optimized phased-array design (0.73 MHz, 128 elements, 381 m element diameter) achieved a focal region at the hypothalamic target with a full width at half maximum of 0.67 mm, a blob count of 1, and a targeting displacement of 0.38 mm when placed 1 mm below the nominal position. Time-reversal phase conjugation further improved confinement and targeting (full width at half maximum: 0.59 mm; displacement: 0.37 mm). Limitations include reliance on a single mouse anatomy, and incorporating additional CT-derived anatomies should enhance generalizability across strains, ages, and sexes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/727023v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@62de15org.highwire.dtl.DTLVardef@e26e57org.highwire.dtl.DTLVardef@1ba4893org.highwire.dtl.DTLVardef@f2c77a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA CT-based acoustic simulation and machine-learning framework was developed to optimize bowl-shaped phased-array transducers for mouse hypothalamic tFUS neuromodulation. C_LIO_LIRandom Forest surrogate models coupled with NSGA-II efficiently identified optimized array designs across frequency, element count, and element diameter. C_LIO_LIThe optimized phased-array design produced a compact hypothalamic focus with submillimeter targeting displacement, with further confinement achieved using time-reversal phase conjugation. C_LI

bioengineering↗

bioRxiv2026

Disentangling polymer confinement from specific-folding interactions reveals the drivers of E. coli chromosome organization

The three-dimensional organization of the bacterial chromosome is critical for gene regulation. Chromosome conformation capture (Hi-C) has enabled genome-wide mapping of chromosomal folding, yet ensemble-averaged contact maps entangle biologically specific-folding interactions (SFIs) with nonspecific polymer compaction and mask single-cell heterogeneity. Here, we developed a polymer-based simulation framework in E. coli to address these limitations. We found that a null model of 300,000 random polymer configurations recapitulated the global chromosomal organization observed in Hi-C data, establishing that most Hi-C signals reflect generic polymer behavior in a confined volume. Contrasting null-model predictions with experimental Hi-C data isolated a small subset of SFIs (< 7%) and generated a specific-fold ensemble of 20,000 single-cell conformations that reproduced chromosomal interaction domains and single-cell heterogeneity. SFIs were enriched in the ter region, reduced nucleoid accessibility, colocalized with cryptic prophages, and depleted in positively supercoiled regions. H-NS and MatP emerged as major chromosome-wide and local determinants of SFIs, respectively. Furthermore, high-SFI regions correlated with stress-adaptive genes, whereas low-SFI regions harbored housekeeping genes. Together, our results established that a small number of biologically encoded SFIs superimposed on a polymer background shape the E. coli chromosome and gene expression, providing a quantitative framework for dissecting chromosome architecture and function.

genomics↗

bioRxiv2026

NOD2 activation reprograms infiltrating inflammatory monocytes in the Zika virus infected CNS to maintain neural correlates of learning and memory

Zika virus (ZIKV) encephalitis induces cytokine-mediated cognitive deficits which persist long-term. Here, we determined if NOD2-mediated conversion of monocytes from Ly6CHi inflammatory to Ly6CLo anti-inflammatory phenotypes during ZIKV encephalitis preserves neural correlates of learning and memory within the hippocampus. Short-term administration of the NOD2 agonist, muramyl dipeptide (MDP), during peak ZIKV infection prevents synapse elimination and loss of adult hippocampal neurogenesis, without impacting CNS virologic control. Transcriptomic analyses of forebrain immune cells in MDP-treated mice revealed functional modulation of infiltrated monocytes and T cells, reducing their expression of pro-inflammatory cytokines, with limited effects on microglia, compared to controls. Notably, NOD2 activation in peripheral immune cells alone balances innate immune signals, preserving synapses, and increasing macrophage phagocytic capacities that do not target synapses. Our findings identify infiltrating Ly6CHi monocytes as key drivers of long-term cognitive dysfunction following ZIKV encephalitis and as potential therapeutic targets for limiting synapse loss. HighlightsO_LINOD2 activation via MDP phenotypically shifts monocyte subsets from inflammatory to anti-inflammatory during the acute phase of ZIKV encephalitis. C_LIO_LIShort-term MDP administration increases phagocytic machinery and reduces inflammatory cytokine/chemokine production within macrophage populations. C_LIO_LISynapse elimination is attenuated within the hippocampus of ZIKV-infected animals treated with MDP. C_LIO_LIMDP derived effects are mediated through peripherally derived immune cells. C_LI

immunology↗

bioRxiv2026

Joint enzyme-reaction retrieval and catalytic optima prediction via multimodal fusion

MotivationEnzyme-reaction retrieval is increasingly used to prioritize candidate biocatalysts for experimental follow-up, where useful recommendations should indicate not only whether an enzyme can catalyze a target reaction but also under which pH and temperature conditions it should be tested. Existing retrieval models optimize catalytic matching scores, whereas catalytic optima predictors are typically developed as enzyme-level regressors because public pH and temperature annotations are sparse and often available only at the enzyme or EC-associated record level. This separation leaves a practical gap: high-ranking enzyme-reaction pairs are not evaluated for condition suitability, and enzyme-level optima predictions do not use the reaction context being retrieved. ResultsWe present GERO, a multimodal fusion framework that uses feature-gated cross-modal fusion to integrate global enzyme sequence semantics, sequence-derived pocket geometry, and molecular reaction representations for condition-aware enzyme-reaction retrieval and catalytic optima estimation with reaction context. To evaluate this setting, we define the tolerance-restricted hit rate (Hit@k-TR), which requires both top-k retrieval of the correct candidate and condition prediction within predefined tolerances. Across enzyme- and reaction-similarity splits, GERO improves Hit@k-TR over two-stage retrieval-then-prediction baselines. Representative benchmark examples and an iodinin biosynthesis case study further illustrate GEROs ability to provide candidate rankings together with plausible assay-condition estimates for downstream experimental prioritization. Availability and implementationSource code is available at https://github.com/ykxhs/GERO. Contactliujuan@whu.edu.cn Supplementary informationSupplementary data are available at XXXX online.

bioinformatics↗

bioRxiv2026

The Magnaporthe oryzae Effector AvrPii Attenuates Rice Immunity by Targeting the Calcium-Associated ANK Protein AVIN8

Rice blast, caused by the fungus Magnaporthe oryzae, poses a severe threat to global rice production. Although numerous M. oryzae effectors have been identified, the molecular mechanisms remain poorly understood. The effector AvrPii triggers ETI upon recognition by NLR receptor Pii and has been shown to target host exocytosis and oxidative metabolic pathways to suppress immunity. Here, we identify AVIN8 (AvrPii-interacting protein 8) as a new target of AvrPii. AVIN8 is an ankyrin-repeat (ANK) protein localized to the plasma membrane and nuclear envelope, with sequence similarity to known ANK calcium channels. AVIN8 expression is induced during early M. oryzae infection. Overexpression of AVIN8 enhances blast resistance, whereas its silencing increases susceptibility. AVIN8 promotes chitin-triggered ROS production in a Ca2+-dependent manner. In contrast, AvrPii impairs Ca2+ influx and chitin-triggered ROS burst. Our findings reveal a virulence strategy in which M. oryzae effector AvrPii hijacks the Ca2+ influx-associated ANK protein AVIN8 to suppress early calcium and PTI signaling in rice.

plant biology↗

bioRxiv2026

ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition

The signaling molecules guanosine 5'-tri/diphosphate 3'-diphosphate, (p)ppGpp, control bacterial protein synthesis rates and cell growth by targeting transcription, translation, NTP synthesis, and other functions. In lineages like E. coli, (p)ppGpp produced in response to charged-tRNA deficiency directly targets transcribing RNAP polymerase (RNAP) to match its pace to the pioneering ribosome on the nascent RNA (transcription-translation coupling). However, the mechanism by which (p)ppGpp slows RNAP is poorly defined. (p)ppGpp may allosterically stimulate RNAP pausing, inhibit catalysis, promote backtracking, compete for substrate GTP, inhibit GTP synthesis, or uncouple transcription-translation by inhibiting translation. Using a combination of cryo-EM, biochemical assays, and quantitative nascent elongating transcript sequencing (qNET-seq), we establish that (p)ppGpp allosterically regulates pausing and nucleotide addition via distinct motions of the RNAP swivel module and both competes with and lowers GTP in vivo. (p)ppGpp stimulates swiveling at pause sites to delay escape but may also inhibit counter-swiveling required in every round of nucleotide addition. HighlightsO_LIppGpp biases RNAP toward swiveling and away from a catalytically-competent state C_LIO_LIppGpp effects on RNAP conformation explain ppGpp stimulation of RNAP pausing C_LIO_LIppGpp stimulation of RNAP pausing in vivo is mediated mainly by reduced GTP levels C_LIO_LIppGpp may allosterically slow RNAP and increases gene occupancy in vivo C_LI

molecular biology↗

bioRxiv2026

In-situ structure of the flagellar export apparatus in Borrelia burgdorferi

The transmembrane export apparatus is a conserved core of bacterial type III secretion systems, shared by the flagellum and injectisome. Powered by the proton-motive force (PMF), this machinery translocates protein substrates across the bacterial envelope to support motility and virulence. However, its assembly and operation within native membranes remain poorly understood. Here, using in-situ single-particle cryo-electron microscopy, we resolve near-atomic-resolution structures of the flagellar export apparatus within the periplasmic flagellar motor of the Lyme disease spirochete Borrelia burgdorferi. Structural and genetic analyses suggest that coordinated, stepwise assembly of the flagellar export apparatus and MS-ring drives local deformation of the cytoplasmic membrane through extensive protein-lipid-protein interactions, constructing a funnel-shaped conduit optimal for substrate translocation. In addition, a conserved hydrophilic pathway lies within core export protein FlhA, with key acidic residues essential for export activity and supporting PMF-driven substrate translocation. Together, these findings establish a mechanistic framework for export apparatus assembly and energy transduction, defining core principles of type III secretion.

microbiology↗

bioRxiv2026

Reversible in vivo regulation of drug metabolizing enzyme CYP1A2 activity through a dTAG knock-in strategy

Drug-metabolizing enzymes determine therapeutic exposure, efficacy and toxicity, but defining their isoform-specific functions in vivo remains challenging. Cytochrome P450 enzymes (P450s) are central to drug metabolism and pharmacokinetics (DMPK) and mediate the phase I metabolism of [~]75% of all marketed drugs. However, conventional knockout models can induce develop-mental and compensatory adaptations, and selective inhibitors are unavailable for many P450 isoforms. Here, we report the use of an inducible chemical-genetic platform for acute and specific degradation of the endogenous P450 enzyme Cyp1a2 in mice. Using CRISPR-Cas9-mediated knock-in editing, we introduced an FKBP12F36V degron into the endogenous Cyp1a2 locus to generate Cyp1a2dTAG mice. Treatment with the dTAG degrader dTAG-13 recruited an E3 ubiquitin ligase to CYP1A2dTAG, resulting in rapid and reversible proteasomal depletion of CYP1A2dTAG in vivo. Temporally controlled CYP1A2dTAG loss altered caffeine pharmacokinetics as expected, validating this model as a functional tool for DMPK studies. By enabling reversible suppression of drug-metabolizing enzymes without permanent deletion or chronic inhibitor exposure, this work establishes targeted protein degradation as a broadly adaptable strategy for studying drug metabolism in vivo and provides a foundation for extending inducible DMPK control to other P450s, conjugating enzymes and transporters.

pharmacology and toxicology↗

bioRxiv2026

Engineering a pacemaker-driven human mini-heart guided by spatial multi-omics of sinoatrial node development

The human sinoatrial node (SAN) functions as the primary pacemaker of the heart and coordinates the hierarchical electrical activity that drives cardiac contraction. However, experimental systems capable of reconstructing pacemaker-driven cardiac organization in human tissues remain limited. Here we integrate spatial multi-omics of the human fetal SAN with stem-cell engineering to generate pacemaker organoids ("Sinoids") and assemble them into a pacemaker-driven human mini-heart composed of sinoatrial, atrial and ventricular cardiac modules. High-resolution spatial transcriptomics and single-nucleus multi-omic analyses of human fetal SAN tissues identify regulatory pathways guiding pacemaker lineage specification, which we leverage to engineer human pluripotent stem cell-derived SAN organoids with robust pacemaker identity and electrophysiological activity. When integrated with atrial and ventricular cardioids, Sinoids initiate and coordinate electrical activation across assembled cardiac tissues, establishing directional propagation of electrophysiological signals within structured mini-heart organoids. Combining AI-guided perturbation modeling with functional validation further identifies conserved regulatory pathways controlling pacemaker specification and regionalization, including YAP-TEAD and NRG-ERBB signaling. Together, these results establish a multi-omic-guided strategy for engineering pacemaker tissues and reconstructing cardiac conduction hierarchy in vitro. The pacemaker-driven mini-heart platform provides a modular human cardiac system for studying pacemaker biology, modeling arrhythmia mechanisms and enabling electrophysiological drug discovery.

bioinformatics↗

bioRxiv2026

Early-life mucosal T cells direct intestinal stem cell fate via a coordinated developmental program

Although early-life immunity was once considered immature, the human fetal immune system is dynamic and compartmentalized by the second trimester. By 21 weeks of gestation, T lymphocytes become a major immune population in the fetal small intestine (SI), yet their functional roles within this tissue remain largely undefined. To explore their unique contributions to intestinal development, we established an ex vivo co-culture system in which mucosal T cells isolated from fetal, neonatal, or adult SI donors were cultured with tissue-derived 3D SI organoids derived from various ages. Homeostatic early-life (fetal and neonatal) SI T cells uniquely promoted organoid generation, a metric of stem cell renewal, by upregulating cell cycle-associated gene programs. These early-life T cells also directed intestinal stem cell differentiation toward the secretory lineage in both growth and differentiation phase, highlighting that T cells poise stem cells to adopt secretory fates. T cells from infants with necrotizing enterocolitis (NEC) - an inflammatory intestinal disease affecting predominantly preterm infants - failed to activate these same programs, suggesting a pathologic role for T cells in NEC. T cells from the adult SI similarly failed to support organoid growth or differentiation, revealing developmentally specialized, nonimmune functions for early-life T cells in the intestine. Similarly, T cells derived from cord blood did not enhance organoid generation, indicating that this function is not necessarily a generalized feature of early-life T cells but rather is restricted to mucosal T cells. Organoids derived from adults or NEC, however, could re-enter regenerative states when co-cultured with fetal T cells, indicating that fetal T cells can restore stem cell self-renewal across developmentally and disease-imposed states. We further identified that T cell-derived soluble factors alone were insufficient to modulate intestinal stem cell fate, implying the need for physical interactions. Concordant with this finding, we report that T cells heavily localize to the stem cell niche during prenatal development, where they express factors involved in Notch, Wnt, and growth factor signaling to support fetal stem cell function. Collectively, these findings reveal a coordinated developmental program in which fetal SI T cells balance stem cell self-renewal and differentiation, identifying a developmental immune-epithelial axis that can be harnessed to restore intestinal regeneration.

immunology↗

bioRxiv2026

ProteinFlux: accurate, rapid and scalable generative prediction of protein dynamics driven by post-translational modifications

The function of proteins, the building blocks of life, in health and disease depends not only on their 3D-conformational states but most importantly on the dynamic transition between states controlled by a wide array of post-translational modifications (PTMs). Recent major advances have been made in our ability to predict static 3D structures; however, understanding and predicting the impact of PTMs on protein conformational dynamics remains a major question and challenge in the field. Molecular dynamics (MD) simulation remains the major computational approach for studying protein dynamics. However, the high computational cost, lack of integration of PTMs as conditioning inputs and inefficient generation of continuous protein dynamics largely precludes PTM-regulated conformational dynamics and the study of slow conformational processes. To address this critical bottleneck, we developed ProteinFlux, a flow-matching generative framework that links PTM-conditioned conformational dynamics to evolutionary constraints encoded by PTM sites. Evolutionary information plays a critical role in capturing conformational dynamics beyond sequence identity, and PTM sites inherently encode evolutionary constraints critical to protein functional regulation. We therefore built FluxSite, a dual-modal PTM site predictor that integrates sequence evolutionary information and 3D structural features to generate a continuous conditional signal encoding conservation and functional importance for each predicted site. FluxSite achieves robust generalization across 18 PTM types and 30 disease-associated proteomes. ProteinFlux generates phosphorylation-conditioned, all-atom conformational trajectories across diverse protein fold classes, faithfully reproducing both thermodynamic properties such as free energy landscapes and kinetic features such as conformational transition pathways. It outperforms state-of-the-art predictors while achieving inference speeds several orders of magnitude faster than traditional MD. In addition, we introduce DynaMo-phos, a benchmark dataset of phosphorylated protein MD simulations. Together, ProteinFlux, FluxSite and DynaMo-phos provide a scalable, high-throughput platform for elucidating PTM-driven conformational mechanisms, with potential applications across allosteric drug design, functional annotation of disease-associated modifications and mechanism-guided therapeutic development.

bioinformatics↗

bioRxiv2026

Lense: Optimizing data preprocessing in single-cell omics using LLMs

Data preprocessing is critical for single-cell omics analyses, but default pipelines often underperform on diverse datasets, especially from emerging platforms like spatial transcriptomics. We introduce Lense, a language-model-guided method that automatically selects optimal preprocessing by comparing plots that visualize low-dimensional representations across pipeline variants. Integrated with Seurat, Lense streamlines analysis and improves preprocessing robustness without requiring manual tuning. Biographical NoteJingyun Liu is a Masters student in the Department of Biostatistics and Bioinformatics at Duke University. Dr. Zhicheng Ji is a tenure-track Assistant Professor in the Department of Biostatistics and Bioinformatics at Duke University. His research focuses on artificial intelligence and statistical modeling for single-cell genomics, spatial genomics, and biomedical imaging.

bioinformatics↗

bioRxiv2026

Organoid modeling of tumor-associated macrophages reveals phagocytosis checkpoint blockade-induced conversion to an immunosuppressive SPP1+ phenotype

Tumor-associated macrophages (TAM) exert essential functions during the immune response to cancer. However, investigations of TAM within a native human tumor microenvironment (TME) have been impeded by a lack of appropriate model systems. Here, patient-derived organoids (PDO) from air-liquid interface (ALI)-grown tumor fragments, containing a human TME that encompassed stroma and immune subsets, robustly preserved TAM that were maintained by endogenous CSF-1 and appropriately responded to polarization signals. Antibody blockade of the CD47 regulatory checkpoint in organoids stimulated phagocytosis and remodeled TAM cytokine secretion profiles that were confirmed in anti-CD47 phase I trial patients. Amongst PDO histologies screened, anti-CD47 tumor killing was notable in clear cell renal cell carcinoma (ccRCC) which was associated with increased TAM infiltration. PDO contained diverse previously described TAM subsets; however, anti-CD47 reprogrammed organoid TAM toward an immunosuppressive SPP1+ phenotype, highlighting a negative feedback mechanism. Our findings uncover a resistance circuit engaged by macrophage checkpoint blockade and position ALI PDO as a robust translational platform for dissecting human macrophage biology and informing precision immunotherapy.

cancer biology↗

bioRxiv2026

NFIC-mediated CaSR endocytosis defines a hyperactive TOMM20highCHGAhigh oxyphil cell state as a pathological driver of autonomous secondary hyperparathyroidism

Secondary hyperparathyroidism (SHPT) is a debilitating complication of chronic kidney disease. Its clinical management is frequently compromised by calcimimetic resistance, a refractory state primarily driven by the progressive downregulation of the membrane calcium-sensing receptor (CaSR). Despite the centrality of CaSR as a therapeutic target, the mechanisms governing its aberrant expression and membrane localization remain incompletely elucidated. Here, we generated a single-cell transcriptomic atlas of human parathyroid tissues from SHPT and primary hyperparathyroidism (PHPT) patients, uncovering a unique stromal-immune niche that is specifically induced by uremic stress in SHPT. Our data also observed a striking dissociation between CaSR mRNA and its abundance as a membrane protein in SHPT tissues. Pseudotime trajectory analysis showed a progressive decline in CaSR pathway activity and a concomitant increase in endo-lysosomal activity along the trajectory, terminating in pathological oxyphil cells as the endpoint of chief cell differentiation in SHPT. Mechanistically, Nuclear Factor I C (NFIC) transcriptionally activated clathrin light chain B (CLTB) and Ras-related protein Rab7a (RAB7A) to trigger clathrin-mediated endocytosis and lysosomal degradation of CaSR, thus reducing its membrane abundance. This degradative program was further validated by multiplex immunofluorescence in TOMM20highCHGAhigh pathological oxyphil cells in human SHPT tissues. To translate these mechanistic findings into a clinically actionable strategy, we repurposed the clinically approved lysosomal inhibitor hydroxychloroquine (HCQ) to block this CaSR degradation pathway. In patient-derived xenograft (PDX) mouse models, co-administration of HCQ and cinacalcet acted synergistically to restore membrane CaSR expression, normalize serum PTH and calcium levels and suppress parathyroid tumor growth more effectively than monotherapies. Collectively, our single-cell-guided study identifies an NFIC-driven endo-lysosomal program as a previously unrecognized mechanism underlying CaSR downregulation and calcimimetic resistance in SHPT, and establishes HCQ repurposing as a clinically tractable therapeutic strategy for patients with refractory SHPT.

cell biology↗