Biology subjects

Liu, J.

Publications and source records attributed to Liu, J..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Circulating APOH promotes aortic dissection by activating the vascular smooth muscle cell NR5A1-PPARγ pathway.

IntroductionsAortic dissection (AD) is a life-threatening vascular disease with limited therapeutic targets. Apolipoprotein H (APOH), a circulating glycoprotein implicated in lipid metabolism, has not been studied in AD. MethodsPlasma APOH levels and aortic deposition were examined in AD patients. A {beta}-aminopropionitrile (BAPN) and angiotensin II (Ang-II)-induced mouse AD model with AAV-mediated Apoh knockdown was used to evaluate survival, aortic dilation, and extracellular matrix remodeling. Transcriptomic profiling, chromatin immunoprecipitation, and gene silencing in human aortic vascular smooth muscle cells (HAVSMC) were performed to dissect the mechanism. PPAR{gamma} agonist rescue was conducted in vivo. ResultsAPOH was elevated in plasma and deposited in AD aortas. Apoh knockdown improved survival, reduced AD incidence and ascending aortic dilation, and attenuated elastic fiber disruption and collagen deposition. Transcriptomics revealed enrichment of the PPAR pathway. APOH promoted HAVSMC phenotypic switching from a contractile to a synthetic state, decreasing ACTA2/TAGLN and increasing OPN/MMP9. Mechanistically, APOH upregulated NR5A1, which directly bound the PPAR{gamma} promoter to enhance PPAR{gamma} and FABP4 expression. Silencing NR5A1 or PPAR{gamma} reversed APOH-induced phenotypic switching and inflammation. In vivo, PPAR{gamma} agonist diminished the protective effects of Apoh silencing. ConclusionAPOH promotes AD progression through the NR5A1-PPAR{gamma} axis, driving vascular smooth muscle cell phenotypic switching and inflammation, and represents a potential therapeutic target. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/739043v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@6c4196org.highwire.dtl.DTLVardef@145f5a2org.highwire.dtl.DTLVardef@19bdborg.highwire.dtl.DTLVardef@19f5019_HPS_FORMAT_FIGEXP M_FIG C_FIG Circulating APOH promotes aortic dissection through the NR5A1-PPAR{gamma} axis in human aortic vascular smooth muscle cells. Clinical observations showed that plasma APOH levels were elevated in patients with aortic dissection. Circulating APOH acts on human aortic vascular smooth muscle cells (HAVSMC) and upregulates NR5A1, which binds to the PPARG promoter and enhances PPAR{gamma} transcription. Activation of the NR5A1-PPAR{gamma} signaling axis promotes the phenotypic transition of HAVSMCs from a contractile phenotype to a synthetic phenotype, as indicated by decreased ACTA2 and TAGLN expression and increased OPN and MMP9 expression, accompanied by enhanced production of the inflammatory mediators IL-6, MCP-1, and TNF-. Silencing NR5A1 or PPAR{gamma} reverses APOH-induced phenotypic switching and inflammatory responses, supporting the critical role of the NR5A1-PPAR{gamma} axis in APOH-mediated vascular injury.

genomics↗

bioRxiv2026

Diagnostic Performance of Fluorescence-Based Rapid On-Site Specimen Evaluation for Helicobacter pylori Antimicrobial Susceptibility Testing Before and After Algorithm Optimization: A Two-Round Comparative Study

ObjectiveThis study was designed to evaluate the diagnostic performance of fluorescence-based rapid on-site specimen evaluation (F-ROSE) for antimicrobial susceptibility testing of Helicobacter pylori (H. pylori) and to compare test performance before and after iterative optimization of fluorescence image acquisition and of the artificial intelligence (AI) recognition algorithm, using two consecutive rounds of paired testing, so as to provide trial data supporting clinical implementation of rapid susceptibility testing. MethodsForty patients with a urea breath test (UBT) or rapid urease test (RUT) positive for H. pylori within the preceding 2 weeks, together with strongly positive endoscopic findings, were prospectively enrolled. In order of enrollment they were allocated to two rounds in which F-ROSE was compared with culture-based susceptibility testing. Twenty patients were tested in round 1 on an automated fluorescence immunoassay scanner running the original algorithm; a further 20 were tested in round 2 with the optimized algorithm. With in vitro culture and E-test as the reference standard, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy of F-ROSE were calculated for each round for amoxicillin, levofloxacin hydrochloride and clarithromycin, and agreement between methods was assessed with Cohens kappa. Receiver operating characteristic (ROC) analysis was used to identify the optimal cutoff of the fluorescence residual rate (FRR) and to determine how far threshold adjustment improved performance. ResultsCulture succeeded in 15 patients in round 1 and in 14 patients in round 2, leaving 29 evaluable samples. Overall diagnostic performance after algorithm optimization was clearly better than before. Pooled across the three antibiotics, sensitivity was 92.9%, specificity 71.0% and accuracy 77.8% before optimization; after optimization sensitivity rose to 100.0%, specificity increased slightly to 74.2% and accuracy to 81.0%. NPV reached 100.0% for all three agents after optimization, and no resistant isolate was missed. The gain was largest for clarithromycin, for which sensitivity rose from 85.7% to 100.0%, accuracy from 66.7% to 78.6% and kappa from 0.348 to 0.571, indicating a clear improvement in agreement between the two methods. ROC analysis showed that drug-specific optimal cutoffs derived from the Youden index improved specificity appreciably compared with the uniform 50% FRR threshold currently applied, the gain being most evident for levofloxacin hydrochloride. ConclusionsWith sharper fluorescence images and an improved AI recognition algorithm, F-ROSE performs better in H. pylori susceptibility testing, and the reduction in missed resistant strains is particularly noteworthy; the assay is therefore a plausible option for rapid susceptibility screening in clinical practice. Multicenter studies with larger samples are still required to confirm the stability of the technique.

microbiology↗

bioRxiv2026

ER Stress-Response Signaling Regulates Chamber-Specific Growth between Right and Left Ventricles during Postnatal Development.

BackgroundDifferential growth between the left (LV) and right ventricles (RV) is a cornerstone of normal heart morphogenesis after birth, leading to the relatively larger and dominant LV over RV in the adult heart regarding size and function. Yet, little is known about the factors that regulate this chamber-specific growth. MethodsWe used both loss-and gain-of-function mouse models, achieved through genetic or pharmacological manipulation of IRE1 or Xbp1 in cardiomyocytes. We also used primary cultured neonatal cardiomyocytes to explore the roles of IRE1, spliced Xbp1 (sXbp1: activated form), and newly identified sXbp1 downstream targets. In addition, we generated heart-specific mosaic mutant mouse models using CRISPR/Cas9/AAV9-based somatic mutagenesis to elucidate the roles of sXbp1 downstream targets in cardiomyocytes. ResultsPharmacological inactivation of IRE1 and genetic depletion of Xbp1 resulted in a smaller LV size, due to decreased cardiomyocyte proliferation and hypertrophic growth, as well as increased cardiomyocyte death. These effects were not observed in the RV. Cardiomyocyte-specific induction of IRE1 or sXbp1 led to increased ventricular size in both ventricles, through enhanced cardiomyocyte proliferation and hypertrophic growth in both LV and RV, and reduced apoptosis in the RV. We identified two ER resident transmembrane proteins, Vimp and Rpn2, as direct binding partners of sXbp1 in targeted gene regulation at the chromatin level. CRISPR/Cas9/AAV9-based somatic mutagenesis mouse models for Vimp and Rpn2 revealed that both genes regulate cardiomyocyte proliferation, hypertrophic growth, and death. We also observed accumulated misfolded proteins in these two mutant hearts. Conclusions We demonstrate that the IRE1-Xbp1-Vimp/Rpn2 axis regulates differential ventricular size between LV and RV during postnatal development by orchestrating cardiomyocyte proliferation, hypertrophic growth, and death through regulating protein homeostasis. Clinical PerspectiveO_ST_ABSWhat Is NewC_ST_ABSO_LIIRE1-Xbp1 axis is dominantly activated in the LV cardiomyocyte during the postnatal period in mouse heart. C_LIO_LIIRE1-Xbp1 mediated ER stress signaling increases cardiomyocyte proliferation and hypertrophic growth and decreases apoptosis in the postnatal period. C_LIO_LIActivated Xbp1 directly regulates LV-specific cardiomyocyte protein homeostasis via interaction with ER membrane targeted Vimp and Rpn2. C_LI What Are the Clinical Implications?O_LIDifferential heart growth patterns between the LV and RV are critical for normal morphogenesis and function of each ventricle. C_LIO_LIControl of protein homeostasis by modulating ER stress signaling could be a potential therapeutic approach for single-chamber heart diseases. C_LI

developmental biology↗

bioRxiv2026

Intrinsic ignition-based propagation networks reveal hierarchical propagation pathways of spontaneous activity in the human brain

Directed communication across brain regions is fundamental to human brain function, yet how local spontaneous activity links to directed whole-brain propagation patterns remains elusive. Prior studies have characterized local propagation events and global wave-like dynamics, but a framework linking local events, interregional propagation pathways, and canonical large-scale propagation patterns remains lacking. Using resting-state functional MRI data from the Human Connectome Project 7T cohort and an intrinsic ignition framework, we quantified cascades of suprathreshold activity events and constructed directed propagation probability networks. We found spatially heterogeneous regional propagation preferences, with high outgoing propagation preferences predominantly localized in somatomotor, visual, and default-mode regions. At the functional system level, propagation modules broadly separated visual, somatomotor, dorsal attention, and ventral attention networks from association systems. Regional stepwise propagation pathways were aligned with the principal functional gradient, and greater hierarchical separation between regions was associated with longer propagation distance. These pathways formed two canonical propagation patterns linking primary and association systems, with somatomotor regions preferentially initiated in bottom-up propagation, default-mode regions in top-down propagation, and attention networks occupying intermediate positions. Notably, the two patterns were not simple mirror images, with top-down propagation showing substantial deviations within somatomotor and visual systems. These findings were replicated in an independent cohort. Moreover, individual propagation architecture predicted cognitive performance and tobacco-use behavior. Collectively, our findings provide cross-scale insights into spontaneous activity propagation in the human brain by bridging local ignition events with hierarchical whole-brain propagation pathways and behaviorally relevant individual differences. SignificanceSpontaneous brain activity is often quantified by the temporal synchronization between regions, but this approach does not show how local activity propagates across the brain. We used an interpretable ignition framework to link local spontaneous events and their cascades to directed whole-brain propagation patterns. This approach revealed outgoing propagation preferences of primary and default-mode regions, a modular architecture separating primary and attentional systems from association systems, and two canonical propagation patterns aligned with the brains functional hierarchy. These two patterns were not simple mirror images, indicating partially distinct bottom-up and top-down routes. Individual propagation architecture also predicted cognitive performance and tobacco-use behavior. These findings provide a path-based view of spontaneous brain dynamics.

neuroscience↗

bioRxiv2026

Rational and computation-assisted engineering of a compact and efficient StaCas9 genome editor

Type II-A CRISPR-Cas9 nucleases are widely used for genome editing, yet their functional diversity and therapeutic potential remain incompletely explored. In this study, we systematically analyzed natural variation in PAM recognition among SaCas9 orthologs and identified StaCas9 as a compact and efficient nuclease recognizing an NNG PAM. Structural and sequence analyses revealed that S983 within the PAM-interacting domain contributes to the PAM preference of StaCas9. StaCas9 enabled efficient genome editing across multiple endogenous loci in human cells and achieved high-efficiency disruption of the therapeutically relevant PCSK9 gene, supporting its potential for gene therapy. Furthermore, guided by structural insights, we significantly enhanced the editing activity of StaCas9. Together, these results expand our understanding of PAM recognition in type II-A Cas9 nucleases and establish StaCas9 as a high-performance genome-editing tool for therapeutic applications.

genomics↗

bioRxiv2026

EBD-DTI: Episodic Bridge Diffusion for Zero-Shot Cold-Start Drug-Target Interaction Prediction

Predicting drug-target interactions (DTI) for entirely unseen drugs or proteins--the cold-start problem--remains a critical challenge in computational drug discovery. While sequence-based methods naturally support zero-shot generalization, they often ignore relational topology, and existing graph-based approaches either rely on global diffusion that blurs the boundary between inductive and transductive evaluation or require a few known interaction samples at test time (few-shot). We present EBD-DTI, a framework that enables zero-shot inference in graph-based DTI models without requiring any known interactions for unseen entities. The key innovation is episodic cold-start training : at each epoch, a random subset of training entities is masked and treated as pseudo-cold, forcing the model to learn cold-start inference with explicit gradient supervision. A bridge-conditioned local subgraph, together with multi-hop diffusion, provides cold entities with relational context from their nearest observed neighbors. Experiments on three benchmarks (BioSNAP, BindingDB, and DrugBank) demonstrate that EBD-DTI achieves competitive or superior performance compared to state-of-the-art methods under strict zero-shot evaluation, with episodic training improving AUC by up to 12%.

bioinformatics↗

bioRxiv2026

Inflammatory arthritis disrupts ocular immune privilege by compromising blood-retinal barrier integrity and promoting uveitogenic T cell recruitment

Inflammatory arthritis and uveitis frequently co-exist, yet the mechanisms linking joint and ocular inflammation remain ill-defined. Here, we investigated how inflammatory arthritis influences ocular immune homeostasis using murine models of antigen-induced arthritis and collagen-induced arthritis. Arthritis promoted the accumulation of T cells, myeloid cells, and neutrophils within the vitreoretinal compartment, without progression to overt clinical uveitis. Ocular leukocyte recruitment was dynamically coupled to arthritis activity, resolving with remission of joint inflammation and recurring during arthritic flares. The magnitude of ocular immune perturbation correlated with arthritis severity, being enhanced in IL-27R-deficient mice and markedly reduced in IL-6R-deficient mice. Mechanistically, arthritis increased blood-retinal barrier permeability, demonstrating that systemic inflammation perturbs ocular immune privilege even in the absence of apparent ocular disease. While arthritis alone was insufficient to induce uveitis, it established a permissive ocular microenvironment that selectively enhanced the recruitment of adoptively transferred uveitogenic CD4+ T cells. These findings identify inflammatory arthritis as a systemic driver of subclinical ocular immune dysregulation and reveal a mechanism by which inflammation at a distant site may promote vulnerability to ocular autoimmunity. These data provide a framework for understanding immune dysregulation at the joint-eye axis and highlight cytokine pathways that may be targeted to preserve ocular immune homeostasis.

immunology↗

bioRxiv2026

Development of a High-throughput in vivo Assay for the Determination of Adenylation Domain Specificities

Natural product synthesis by non-ribosomal peptide synthetases (NRPS) is greatly defined by the substrate selectivity of the adenylation (A) domains. Previous assays for specificity determination were mainly performed in vitro and were requiring protein purification. In this work, we developed - based on NRPS engineering - a novel in vivo assay suitable for high-throughput application named ASCR (A domain screening). Using the recently described XUT fusion sites, A domains and their upstream condensation domains were assembled as di-domains to characterized NRPS model system, which allowed detection of defined tripeptide products via mass spectrometry directly after cell culture extraction. We evaluated the assay by screening in total 54 A domains from five known and seven uncharacterized NRPS, covering a broad range organism taxonomy and GC content of the investigated NRPS-encoding genes. Additionally, we applied the assay to elucidate and confirm the structures of novel cyclic pentapeptides derived from three novel NRPS from Photorhabdus temperata K122.

biochemistry↗

bioRxiv2026

De novo design of ligand binding and sensing with a physics based generative approach

The de novo design of ligand-binding proteins has tremendous potential to revolutionize biosensor technology, yet converting these designs into functional sensors remains a major challenge due to the need for ligand-induced conformational changes or modulation of protein-protein interactions. Here, we introduce a physics-based generative approach for the de novo creation of proteins that bind small molecules and metal ions. Our method achieves customizable ligand-binding pocket formation in parallel with simulated protein folding, allowing for precise architectural control of the protein-ligand complex and facilitating the development of biosensors based on either ligand-triggered protein reassociation via split-protein reassembly or ligand-induced protein folding. We demonstrate the versatility of our computational method through successful designs targeting five small molecules, including the very small neurotransmitters serotonin and dopamine, and two metal ions. Biophysical characterization confirmed correct ligand binding, and crystal structures closely matched computational models. We demonstrated the biosensor engineering potential of these designs by constructing serotonin and dopamine sensors using a split protein strategy and explored several approaches to enhance sensor activity. Additionally, we developed a zinc sensor through a zinc-induced protein folding mechanism. Overall, our physics-based generative approach provides a robust framework for the de novo design of ligand-binding proteins, opening new avenues for the development of ligand-responsive biosensors.

bioinformatics↗

bioRxiv2026

Mycobacterium tuberculosis Δlsr2 Vaccine Enhances Protection Against Tuberculosis

Tuberculosis (TB) has been a leading cause of death from a single infectious agent for decades. Bacille Calmette-Guerin (BCG) remains both the primary TB vaccine strategy and the oldest vaccine in circulation, with severe limitations in adult populations. Recently, live attenuated vaccine strategies, or generating safe strains of Mycobacterium tuberculosis (Mtb) through genetic engineering, have shown considerable promise. We previously developed an attenuated strain of Mtb lacking the nucleoid-associated protein Lsr2 ({Delta}lsr2) which is also phthiocerol dimycocerosates (PDIM) deficient and induces an immune response that represents an intermediate stage between the parental Mtb strain and BCG. In this study we examined the immune response of {Delta}lsr2 vaccinated mice in comparison to BCG and found a substantially stronger CD4 and CD8 T cell responses from {Delta}lsr2 vaccinated mice. Complementary, we conducted Mtb protection studies in {Delta}lsr2 and BCG vaccinated mice and guinea pigs, where we found that {Delta}lsr2 provided superior protection in both animals. This improved protection is shown with reduced bacterial burden and improved organ pathology in the lungs and spleen. Taken together, our work shows {Delta}lsr2 serves as a promising vaccine candidate for continued preclinical development.

immunology↗

bioRxiv2026

DSPE-PEG does not retain targeting antibodies on LNP surfaces in vivo; a higher molecular weight anchor is required

Extrahepatic delivery of lipid nanoparticles (LNPs) to non-phagocytic cells is a major challenge, with the leading strategy involving surface functionalization with target-specific monoclonal antibody (mAb) ligands. We investigate the stability of mAb-conjugated LNPs using two anchoring systems: the commonly used DSPE-PEG2kDa-maleimide and a block copolymer, PCL5kDa-b-PEG2kDa -maleimide, with the hypothesis that conjugation to a 150,000 Da antibody could overwhelm the relatively small [~]600 Da aliphatic anchor on the PEG-lipid in vivo. Shedding of the mAB would compromise targeting. Conjugation integrity following IV injection was assessed by tagging LNPs and mAbs with metal ion tracers that could be quantified by ICP-MS. Results show that DSPE-PEG-mAb rapidly (within 1h) dissociates from LNPs in blood, leading to accelerated LNP clearance. In contrast, mAbs conjugated using PCL-b-PEG remained stably associated with the LNP over the 24h circulation and clearance of the construct. Results are connected to a thermodynamic model that reproduces experimental findings for PEG-anchor(-mAb) shedding in vitro and in vivo. This study identifies anchoring strength as a critical, unconsidered parameter for in vivo performance when conjugating mAbs to LNPs for extrahepatic delivery. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/736109v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@fd783eorg.highwire.dtl.DTLVardef@e1351borg.highwire.dtl.DTLVardef@165ab26org.highwire.dtl.DTLVardef@1c752a9_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

High Dimensional Immune Profiling Reveals CD39 as a Correlate of Tuberculosis Disease Severity

Immune biomarkers of tuberculosis (TB) disease severity present a challenging area of research that remains poorly understood. New technologies are able to perform larger, unbiased studies that can unravel the complex host-pathogen dynamics occurring during a Mycobacterium tuberculosis infection, the causative agent of TB. In this study, we designed a high dimensional approach combining viable bacterial burden (CFU, colony forming units) with time-of-flight mass cytometry (CyTOF) analysis to profile differences in cell-type abundance and cell-type specific protein expression during states of low, intermediate and high TB disease burden. Broadly, we segregated cell-type specific immune responses into those driven by bacterial burden and/or the mycobacterial infection strain. Interrogating these immune signatures allowed us to identify ATP-catabolizing protein CD39 as a correlate of disease severity. Treatment of mice with a small molecule inhibitor of CD39 promoted effector T cell functions and CD4 T cell expansion during Mtb infection. Collectively, our data defines the differential lung immune environment between various mycobacterial disease severity states and uncovers a potential immune biomarker of infection and therapeutic immunomodulating target to aid in the treatment of TB.

immunology↗

bioRxiv2026

Designing Fidelity of CRISPR-Cas Endonucleases by Kinetic Insights

Finding high-fidelity CRISPR-Cas variants is critical for both the precision of in vitro DNA detection and the safety of in vivo gene-editing therapeutics. However, the large size of the Cas enzyme and the distinct selection criteria between its natural evolution and clinical practice lead to extensive experimental trials and limited success rate for de novo design, directed evolution, protein language model (PLM)-based filtering. Here, we present a PLM-assisted physics-driven approach that utilizes atomistic molecular dynamics simulations and automated path searching to efficiently obtain the complete kinetic insights, including the transition state structures, for the conformational changes of Cas before DNA cleavage. We show that these kinetic insights can pinpoint a few fidelity-diminishing protein residues during the early stage of target recognition, and have led to SpyCas9 and FnCas12a variants with ultra-high fidelity surpassing previously reported counterparts at minimal cost of a few wet-lab trials.

biophysics↗

bioRxiv2026

Unearthing a fungal giant: Dianjunaceae fam. nov., a novel Paleocene lineage of Xylariales harbouring Dianjunus rex gen. et sp. nov.

During mycological surveys in Yunnan Province, China, specimens of a fungus producing massive, upright stromata up to 50 cm high and individually 2.2 Kg in weight were sampled. Through an integrative taxonomic approach combining detailed morphology, multilocus phylogeny (ITS, LSU, RPB2, TUB2), and phylogenomic analyses, this fungus is proposed as the new species Dianjunus rex gen. et sp. nov., the type of the new family Dianjunaceae (Xylariales). Phylogenetic analyses robustly place Dianjunaceae as a distinct sister clade to Graphostromataceae. Divergence time estimation dates the origin of this family to the early Paleocene ([~]65 Mya), coinciding with the post-K-Pg extinction period, when an estimated 75% of all plant and animal species went extinct, and a significant ecological reorganization of life on earth happened. The stromata of D. rex represent the largest fructifications documented within the Ascomycota, significantly expanding the known morphological range of the Xylariales. The study provides a comprehensive description, including a nodulisporium-like anamorph with periconiella-like branching patterns, and discusses the taxons phylogenetic placement, and distinctive morphology. This discovery highlights the unexplored fungal diversity in East Asian forests.

microbiology↗

bioRxiv2026

Astrocyte-to-microglia purinergic signaling mediates synaptic shielding and promotes neuronal activity

How glial cells sense and regulate neuronal hypoactivity remains poorly understood. Using in vivo imaging in anesthetized, sleeping, and behaving mice, we identified a glial purinergic signaling mechanism that converts neuronal hypoactivity into local circuit regulation. Cortical hypoactivity increased spatially confined ATP release through astrocytic pannexin-1 hemichannels, which were structurally enriched near perisomatic parvalbumin-positive boutons. Local ATP release directed microglial process movement and stabilized bulbous endings through microglial P2Y12 signaling, accompanied by localized Ca{superscript 2} activity in microglial processes. Disruption of astrocytic pannexin-1 or microglial P2Y12 impaired bulbous-ending stabilization and abolished rebound increases in neuronal activity during emergence from anesthesia. Similar ATP release and bulbous-ending formation were observed during chemogenetic neuronal silencing or natural sleep in freely behaving mice. These findings identify astrocyte-to-microglia purinergic signaling as a mechanism that converts neuronal hypoactivity into synapse-selective microglial regulation of circuit activity.

neuroscience↗

bioRxiv2026

Culture-Free Rapid Phenotypic Antimicrobial Susceptibility Testing for Helicobacter pylori Based on Fluorescence Rapid On-Site Evaluation Technology: A Preliminary Study

BackgroundPhenotypic antibiotic susceptibility testing (AST) for Helicobacter pylori (H. pylori) has relied on bacterial culture for three decades, requiring 5-7 days to yield results. Genotypic rapid tests can only detect known resistance mutations and fail to reliably identify amoxicillin resistance. To our knowledge, no culture-free rapid phenotypic AST method for H. pylori has been previously reported. MethodsWe developed a phenotypic AST method based on fluorescence rapid on-site evaluation (ROSE) technology that completely bypasses bacterial culture. Gastric mucosal biopsy specimens from 40 H. pylori-positive patients were homogenized and co-incubated with an acridine orange/ethidium bromide (AO/EB)-based viability staining reagent and three first-line antibiotics--amoxicillin, clarithromycin, and levofloxacin--at concentrations corresponding to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints for H. pylori, at 37 {degrees}C for 1 hour. Fluorescence intensity was measured using a microplate reader. A reduction in fluorescence relative to an antibiotic-free control indicated susceptibility, whereas no significant reduction indicated resistance. Conventional culture-based AST (E-test) served as the reference method. The overall concordance rate, sensitivity, specificity, and Cohens kappa coefficient were calculated. ResultsFourteen of the 40 samples had unsuccessful culture and were excluded, leaving 26 samples for statistical analysis of each antibiotic. The overall concordance rates between the ROSE method and culture-based AST were 84.6% (22/26) for amoxicillin, 76.9% (20/26) for levofloxacin, and 69.2% (18/26) for clarithromycin. Cohens kappa coefficients indicated moderate agreement for all three antibiotics ({kappa} = 0.523, 0.539, and 0.412, respectively). Unlike genotypic methods, the ROSE method successfully assessed amoxicillin susceptibility in all 40 patients--a critical first-line antibiotic for which no reliable genetic resistance marker currently exists. The turnaround time was approximately 1 hour (55-65 minutes), compared with 5-7 days for culture-based methods; preliminary estimates indicated a cost reduction of approximately 3,000-5,000 Chinese yuan (CNY) per patient, mainly attributable to the elimination of culture media, prolonged incubation, and repeat clinic visits. ConclusionsThis study reports, for the first time, a culture-free 1-hour phenotypic AST for H. pylori. The method enables same-day, susceptibility-guided treatment decisions, addressing an unmet clinical need spanning three decades. Algorithm optimization and a prospective randomized controlled trial are currently underway to further improve diagnostic accuracy and validate clinical utility.

microbiology↗

bioRxiv2026

Radioligand therapy in combination with CAR T cells overcomes the heterogeneous immunosuppressive prostate tumor microenvironment

177Lu-PSMA-617 (PluvictoTM, Lu-177 RLT) is an FDA-approved targeted radioligand therapy (RLT) for metastatic castration-resistant prostate cancer (mCRPC), but its durability of response to this singular approach poses a challenge to the field. Chimeric antigen receptor (CAR) T cell therapy has revolutionized clinical practice for hematological malignancies, but its clinical development for solid tumors, including mCRPC, has been encumbered by antigen heterogeneity and the immunosuppressive tumor microenvironment (TME). Here, we evaluate the therapeutic combination of Lu-177 RLT and PSCA-CAR T cells to overcome these barriers. In human xenograft and mouse syngeneic prostate cancer models with homogeneous or heterogeneous antigen expression, the sequential administration of Lu-177 RLT, cyclophosphamide (Cy), and PSCA-CAR T cells improves tumor control and prolongs survival compared to monotherapies. Mechanistically, Lu-177 RLT alone or with Cy remodels the TME by promoting pro-inflammatory myeloid responses and activating endogenous T cells, while enhancing CAR T cell activation and effector function. We additionally evaluated 225Ac-PSMA-617 RLT as an emerging approach in combination with CAR T cells and observed anti-tumor responses, supporting its potential as an alternative RLT partner. These findings support RLT as an immune priming strategy to enhance CAR T cell therapy and provide a rationale for clinical translation of this combination in mCRPC. One Sentence SummaryCombining 177Lu-PSMA-617 radioligand therapy with PSCA-CAR T cells improves tumor control and survival in prostate cancer models by overcoming the antigen heterogeneity and reshaping the immunosuppressive tumor microenvironment.

cancer biology↗

bioRxiv2026

SpaGRD deciphers signaling architectures in spatial transcriptomics using graph reaction-diffusion systems

The rapid emergence of spatial transcriptomics offers unprecedented opportunities to study cell-cell communication (CCC) by capturing gene expression alongside spatial context. However, existing CCC inference methods often rely on static, heuristic models that overlook the inherently spatiotemporal dynamics and mechanistic complexity of intercellular signaling, limiting both accuracy and biological interpretability. Here, we present SpaGRD, a first-principles-based method that explicitly models ligand-receptor interactions through partial differential equations derived from Ficks law of diffusion and the mass action law. Leveraging graph signal processing techniques, SpaGRD solves these equations on spatial graphs, providing a principled and generalizable approach to CCC inference. Through extensive simulations, SpaGRD demonstrates superior accuracy and robustness compared to existing methods. Applications to multiple datasets across diverse tissues and platforms reveal dynamic CCC patterns with spatially resolved signaling heterogeneity, providing biologically meaningful insights into cellular coordination and developmental processes. By bridging physical modeling with spatial transcriptomics, SpaGRD provides an accurate, interpretable, and mechanistically grounded framework for advancing quantitative studies of spatiotemporal cell-cell communication.

bioinformatics↗