Biology subjects

Jiang, B.

Publications and source records attributed to Jiang, B..

At least 19 recordsLinked to original sources

bioRxiv2026

A Vma13-targeted thiadiazole-succinimide disrupts V-ATPase dependent arginine-polyamine homeostasis to block Candida albicans escape from macrophages

Invasive candidiasis caused by Candida albicans is a life-threatening nosocomial infection with limited therapies and high morbidity and mortality among immunocompromised patients. Within host phagocytes, C. albicans catabolizes arginine to produce ammonia and fuels polyamine biosynthesis, which correlates with phagosomal alkalinization and yeast-to-hypha morphogenesis, facilitating macrophage escape and systemic dissemination. However, new antifungal strategies blocking this fungal escape remain scarce. Here, we characterize the thiadiazole-succinimide derivative ETSI, an arginine-dependent antifungal small molecule with minimal direct growth inhibition under arginine-free conditions yet robust anti-C. albicans activity in arginine-rich microenvironments mimicking the macrophage intracellular niche. Mechanistically, ETSI targets the vacuolar Vma13 to inhibit vacuolar H-ATPase (V-ATPase), dissipating vacuolar proton (H+) gradients and leading to cytoplasmic H+ retention. The accumulated cytoplasmic H+ traps intracellular ammonia and blocks its external release, while impaired vacuolar metabolite sequestration further triggers cytotoxic accumulation of arginine and polyamine metabolites. This dual metabolic perturbation suppresses phagosomal alkalinization, retains C. albicans in yeast form and blocks macrophage escape. ETSI is the first small molecule blocking C. albicans escape via disrupted Vma13/V-ATPase dependent arginine-polyamine homeostasis. This work identifies an intracellular metabolic vulnerability and establishes a niche-targeted antifungal strategy distinct from classic growth-suppressive drugs for treating invasive candidiasis.

microbiology↗

bioRxiv2026

KRASG12C Inhibition Remodels the Non-Small Cell Lung Cancer Surfaceome to Uncover Targetable Vulnerabilities

Mutant-selective and pan-RAS(ON) multi-selective inhibitors have improved clinical outcomes for patients with RAS-driven cancers; however, adaptive resistance limits the depth and durability of response. Using an integrated genetic, transcriptomic, and mass-spectrometry-based quantitative temporal proteomic platform, we profile the adaptive response to KRASG12C inhibitors (KRASi) in KRASG12C-mutant lung adenocarcinoma models. Our analyses reveal remodeling of signaling pathways and the cell surface proteome, including cell surface proteins selectively upregulated across cell lines, tumor models, and treatment durations. Folate receptor alpha (FOLR1) emerged as a therapeutically actionable target that is significantly upregulated with KRASi and is part of a broader acute cellular state transition characterized by acquisition of an epithelial identity. Combining KRASi with mirvetuximab soravtansine-gynx, a clinically approved FOLR1-targeting antibody drug conjugate, enhanced tumor cell cytotoxicity and deepened response and tumor control in cellular and in vivo models. Additionally, this work represents a comprehensive multi-omic resource characterizing non-genetic temporal adaptation to KRASi for future mechanistic and therapeutic investigations.

cancer biology↗

bioRxiv2026

HER2 mutation-derived neoantigens in NSCLC as actionable targets for TCR therapy

HER2 mutations are oncogenic drivers in 1-6% of non-small cell lung cancers (NSCLC), but therapeutic resistance limits the durability of current HER2-targeted treatments. Here, we identify T-cell receptors (TCRs) targeting recurrent HER2 hotspot mutations as a potential immunotherapeutic strategy for HER2-mutant NSCLC. Using neoepitope prediction and antigen-specific T-cell enrichment, we isolated HLA-A*02:01restricted TCRs recognizing HER2 A775insYVMA, S310F, and G776delinsVC mutations, collectively covering approximately 60% of HER2-mutant NSCLC. These TCRs selectively recognized mutant HER2 epitopes without detectable wild-type reactivity and some displayed cross-recognition of related hotspot variants, expanding the spectrum of targetable tumors. The G776delinsVC-specific TCR also exhibited co-receptorindependent activity showcased by its ability to activate CD4+ T cells. Importantly, timelapse single-cell flow cytometry analyses demonstrated that TCR-engineered T cells repeatedly reacquired activated polyfunctional states following serial antigen stimulation, while serial tumor rechallenge assays confirmed sustained cytotoxic activity across multiple rounds of tumor killing. These findings identify recurrent HER2 mutations as shared immunotherapeutic targets and provide a foundation for the development of TCR-based therapies for HER2-mutant NSCLC.

immunology↗

bioRxiv2026

Uncovering key genes related to potato tuber starch concentration from the tuber bulking, maturation stage to storage

Potato is the worlds fourth major staple crop, and tuber starch is a critical dietary energy source and a food processing raw material. In this study, hybrid progenies of the high-starch cultivar Huasheng No.7 and China main commercial varieties were used as materials, high-throughput sequencing was performed on tuber samples at tuber bulking, maturation and storage stages. Combined with bioinformatics analysis, parent-progeny resequencing, SNP screening, the regulatory mechanism of tuber starch metabolism was explored. The results showed significant stage-specific transcriptional reprogramming in potato tubers: few differentially expressed genes (DEGs) were identified at tuber bulking and maturation stages, but massive transcriptional changes occurred during storage. XET family genes regulated cell wall remodeling and carbon translocation across all stages, and WRKY transcription factors specifically controlled starch homeostasis in stored tubers. The DEGs at different stage were induced by the SNPs from their parent, and the allele from the high-starch parent, Huasheng 7 may contribute the high-starch allele to the offsprings. One key gene, Soltu.DM.02G019910, which encoded {beta}-glucosidase, have a negatively relationship with tuber starch concentration. The low-starch potato breeding tubers shown higher significantly {beta}-glucosidase activity than high-starch breeding population at maturation stage. This study clarifies the molecular regulatory network of potato tuber starch metabolism and screens core regulatory genes from the tuber bulking stage to tuber storage, thereby providing theoretical support and genetic resources for molecular breeding of high-starch and storage-resistant potato varieties.

plant biology↗

bioRxiv2026

A Pro-Regenerative Petroleum Jelly-Based, Copper-Doped Bioactive Glass Ointment for Impaired Wound Healing in Metabolic Syndrome

Chronic wound healing is often impaired in conditions such as metabolic syndrome, requiring effective therapeutic interventions to promote tissue regeneration and repair. In this study, we evaluated the wound healing potential of petroleum jelly (P Jelly)-based bioactive glass ointments (PBGCu) with varying copper concentrations (0, 1, and 3 wt%) in both in vitro and in vivo models of wound healing. PBGCu formulations demonstrated high biocompatibility with human dermal fibroblasts (HDF) and human umbilical vein endothelial cells (HUVEC). Additionally, PBGCu ointments exhibited strong antibacterial activity against Staphylococcus aureus, suggesting their utility for the care of chronic wounds. In both metabolic syndrome mouse and pig models, PBGCu3-treated wounds showed significantly faster wound closure, enhanced epithelial regeneration, and increased dermal thickness compared to saline and P Jelly controls. Histological analysis also revealed 50% increased vascularization (p < 0.0001) and a 90% reduction in scar formation (p < 0.0001) in PBGCu3-treated wounds. These findings show that PBGCu formulations, especially at 3 wt% copper concentration, significantly improve wound healing by promoting epithelial regeneration, dermal tissue formation, and vascularization, while also offering antibacterial protection. The sustained Cu2+ ions release from PBGCu ointments provides long-term support for tissue regeneration, positioning this ointment composition as a promising therapeutic tool for chronic wound management. Future studies will focus on elucidating the underlying mechanisms and evaluating the therapeutic efficacy of PBGCu formulations in infected wounds. HighlightsO_LIDeveloped a Petroleum Jelly-based copper-doped bioactive glass ointment (PBGCu) enabling sustained and controlled Cu{superscript 2} ion release. C_LIO_LIPBGCu significantly accelerated wound closure and improved epithelial and dermal tissue regeneration. C_LIO_LIPBGCu enhanced hair follicle regeneration and tissue remodeling in full-thickness wounds. C_LIO_LIValidated therapeutic efficacy in both mouse and pig models that support translational relevance. C_LIO_LIOffers a simple, low-cost, and clinically adaptable topical formulation for metabolic syndrome-related wound complications. C_LI

bioengineering↗

bioRxiv2026

Hepatic Acetate is an Essential Fuel for the Heart during Energy-Deprived States

Energy supply is fundamental to cardiac performance, yet the mechanisms by which the heart adapts to nutrient scarcity remain incompletely understood. Here, we identify acetate as a pivotal metabolic substrate that sustains cardiac contractile function during fasting-induced energy deficiency. Fasted mice reveal significant elevation of circulating acetate derived from hepatic fatty acid catabolism. Physiological concentrations of acetate alone can maintain ex vivo beating and electrical stability in Langendorff-perfused hearts. Primary mouse cardiomyocytes preferentially utilize acetate under energy-restricted conditions, which is abolished by knockdown of mitochondrial Acss1, the enzyme responsible for converting acetate to acetyl-CoA. Isotopic tracing with 13C-acetate demonstrated selective cardiac uptake during fasting. In vivo, acetate supplementation preserved heart rate and systolic function in fasted wild-type mice but not in Acss1-deficient hearts. These findings reveal an Acss1-dependent metabolic pathway enabling the heart to harness hepatic acetate as an endogenous fuel, representing a nutrient stress-responsive adaptation based on inter-organ crosstalk and implying therapeutic potential of acetate to energy-deficient heart diseases.

biochemistry↗

bioRxiv2026

Daikenchuto modulates gut microbial metabolism to mitigate irinotecan-induced enterotoxicity

Gut microbiota metabolic remodeling is a pivotal determinant in irinotecan-induced enterotoxicity and epithelial damage, although the underlying mechanisms remain unclear. Herein, we discovered that Daikenchuto (DKT), a traditional Chinese prescription for intestinal disorders, alleviated irinotecan-induced enterotoxicity without compromising its anti-tumor efficacy by improving weight loss, diarrhea, intestinal inflammation, and barrier damage, and these effects were partially dependent on gut microbiota. DKT significantly restored microbial tryptophan metabolism in irinotecan-treated rats, which was characterized by the enrichment of Limosilactobacillus reuteri, and elevated levels of indole-3-ethanol (IE) and indole-3-propionic acid (IPA). Multi-omics analysis further revealed a positive correlation between L. reuteri and IE and IPA. Consistent with this, DKT promoted L. reuteri proliferation, leading to the conversion of tryptophan to IE and IPA, which improved epithelial barrier damage in the irinotecan-treated Caco-2 cells. In addition, DKT suppressed the growth of Loop 1 {beta}-glucuronidase ({beta}-GUS)-producing bacteria, such as Escherichia coli. Furthermore, the main constituents of DKT selectively inhibited Loop 1 {beta}-GUS activity independent of the gut microbiota, which reduced the intra-luminal level of 7-ethyl-10-hydroxycamptothecin, the toxic metabolite of irinotecan. Taken together, this study reveals a dual gut microbiota-driven mechanism by which DKT mitigates irinotecan-induced enterotoxicity, which provides a promising strategy for managing chemotherapy-related enterotoxicity.

pharmacology and toxicology↗

bioRxiv2026

Multicopper oxidase mediated single-carbon insertion for skeletal remodeling

Modern drug discovery demands efficient strategies for generating structurally diverse compound libraries. Skeletal editing--a transformative paradigm enabling precise atom-level modifications within molecular frameworks, offers a sustainable alternative to traditional synthetic routes. While carbene insertion-mediated approaches have dominated single-carbon insertion strategies, current methodologies are limited by their reliance on hazardous, unstable carbene precursors and harsh reaction conditions. Herein, we report a multicopper oxidase (MCO)-catalyzed skeletal editing that enables the direct, one-step transformation of phenolic and indole derivatives into functionalized tropones and quinoline analogues through exogenous single-carbon insertion. This platform employs stable and safe nitroalkanes as carbon sources and O2 as the sole terminal oxidant. It accommodates a broad substrate scope and yields products with superior antibacterial activity against to multidrug-resistant strains relative to their parent compounds. This work introduces the first biocatalytic platform for exogenous single-carbon insertion skeletal editing. This sustainable and scalable strategy overcomes key limitations of synthetic approaches, offering efficient skeletal remolding and rapid expansion of bioactive compound libraries. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/714988v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@1f1d09borg.highwire.dtl.DTLVardef@b67c65org.highwire.dtl.DTLVardef@a0cd4dorg.highwire.dtl.DTLVardef@106afe5_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

ATG5 regulates autophagy-apoptosis-ER stress dysregulation in steroid-induced osteonecrosis of the femoral head (SONFH) pathogenesis

The aim is to investigate how ATG5 regulates autophagy, endoplasmic reticulum stress (ERS), and apoptosis in steroid-induced osteonecrosis of the femoral head (SONFH), and to evaluate ATG5-targeted inhibition as a SONFH intervention. Differentially expressed genes in SONFH were screened using GEO dataset GSE74089. Autophagy/apoptosis/ERS pathway activities were analyzed via GSEA, GO/KEGG enrichment, and GSVA. Rat bone marrow mesenchymal stem cells (BMSCs) were isolated for osteoblast modeling. Groups included: control (A), steroid-treated (B, methylprednisolone), and intervention (C, steroid + ATG5-siRNA). Autophagosome formation, apoptosis rate, and ATG5/PERK/LC3 expression were assessed by electron microscopy, flow cytometry, qPCR, and western blotting. Sixty SD rats were divided into three groups (as above). The SONFH model was established via intramuscular methylprednisolone injection, with intervention group receiving ATG5-siRNA. Bone pathology, cell death, and pathway regulation were evaluated using HE/TUNEL staining, electron microscopy, and molecular detection. Transcriptome analysis revealed synergistic activation of autophagy (ATG5/BECN1), apoptosis (CASP3/9/12), and ERS (PERK) pathways in SONFH, with ATG5 strongly correlating with all three. Steroids upregulated ATG5 to overactivate autophagy, triggering PERK-mediated ERS and ERS-specific apoptosis. ATG5-siRNA intervention inhibited autophagosome formation, reduced apoptosis, downregulated PERK, and alleviated trabecular fractures and empty lacunae. ATG5 deficiency blocked PERK signaling, suppressing both autophagic death and ERS-dependent apoptosis.ATG5 drives autophagy overactivation and ERS-apoptosis cascades via PERK pathway activation, constituting a core SONFH mechanism. Targeted ATG5 silencing effectively blocks this pathology, offering novel preventive/therapeutic strategies.

molecular biology↗

bioRxiv2026

An autonomous system for multi-objective continuous evolution at scale

Natural evolution is high-dimensional; organisms adapt to many pressures at once, across substrates, environments, and genetic backgrounds. Yet most directed evolution methods flatten this landscape to a single selection axis, hiding tradeoffs, and limiting what can be learned. Phage-assisted continuous evolution (PACE) is uniquely suited for multivariate selection because horizontal gene transfer couples genotype to propagation and allows the same phage lineage to traverse different selection environments. In practice, implementing this at scale has been prohibitive because each selection demands its own host culture, and every culture must be held for days to weeks within a narrow, infectable density window using continuously responsive bioreactors. In this work, TurboPRANCE is presented as an open-source, queueable robotic platform that integrates [~]200 independently controlled turbidostats with 96 parallel PACE lagoons under closed-loop control. Each turbidostat operates as a fully separate unit that can be equilibrated and initiated on its own schedule, enabling asynchronous starts and sustained operation without intervention. Automated media formulation, programmable dosing, on-deck sterilization, and adaptive scheduling coordinate growth control with the changing needs of the robotic workflow, dynamically adjusting dilution and transfer timing around formulation, sampling, and handling steps to keep each culture at consistent infectable densities despite unpredictable method demands. Cultures can be multiplexed and titrated into lagoons at defined ratios, swapped in and out on a schedule, or kept fully separate across experiments, creating a combinatorial space of selection pressures and programs that is effectively unbounded. Additionally, to enable high-throughput evolutionary tracking that scales with TurboPRANCE, Nanopore long-read sequencing was combined with DeepVariant, a deep learning-based variant caller, enabling population-level tracking of evolving variants. The result is a system that generates high-resolution time-resolvable evolutionary trajectories and large parallel datasets spanning diverse selection regimes, yielding dense, multivariate training data to map and engineer complex fitness landscapes at scale. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/709196v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@b0f8daorg.highwire.dtl.DTLVardef@a1d57eorg.highwire.dtl.DTLVardef@c771aeorg.highwire.dtl.DTLVardef@1f8729a_HPS_FORMAT_FIGEXP M_FIG Turbidostat, Phage, and Robotics-Assisted Near Continuous Evolution (TurboPRANCE) In phage-assisted continuous evolution (PACE), biomolecular activity is coupled to pIII expression, linking function to phage propagation. By altering the host strain, distinct selection pressures can be imposed on the same evolving phage population. In TurboPRANCE, [~]200 selection programs can vary over time, including periodic "drift" (mutagenesis), alternation between pressures, or rotational reassignment of host sources, enabling a combinatorial space of selection pressures. C_FIG

bioengineering↗

bioRxiv2025

The non-kinase function of CDK6 is a key driver of acquired resistance to CDK4/6 inhibitors in Estrogen Receptor-positive breast cancer

The therapeutic efficacy of CDK4/6 inhibitors in ER+ breast cancer (BC) patients is presumed to arise from inhibition of the kinase function of CDK4 and 6 proteins. Despite their initial efficacy, development of acquired resistance to CDK4/6 inhibitors in metastatic ER+ BC patients is nearly universal, commonly through compensatory overexpression of CDK6. Here, we show that primary ER+ tumors show high CDK4 but very low to undetectable expression of CDK6, which suggests that the therapeutic efficacy of CDK4/6 inhibitors in ER+ BC patients is largely driven by inhibition of CDK4, rather than CDK6. Furthermore, we show that overexpression of CDK6 confers acquired resistance to CDK4/6 inhibitors, largely, through a kinase-independent function. Our findings challenge the dogma that CDK4/6-mediated phosphorylation of retinoblastoma protein (pRB) is necessary to ER+ BC cells to progress from G1 to S phase of cell cycle. Consequently, by taking advantage of the non-kinase function of CDK6, ER+ BC cells acquire independence from the kinase function of CDK4 and 6 for cell cycle progression. These findings highlight the limitations of the current standard-of-care treatments, which focus on merely inhibiting the kinase function of CDK4 and 6, and uncover the non-kinase function of CDK6 as a new targetable vulnerability to overcome acquired resistance to CDK4/6 inhibitors in ER+ BC.

cancer biology↗

bioRxiv2025

Neuronal subtype-specific metabolic changes in neurodegenerative and neuropsychiatric diseases predicted via a systems biology-based approach

Understanding how distinct neuronal subtypes contribute to Alzheimers disease (AD) pathology remains a major challenge. Patient-derived induced pluripotent stem cell (iPSC) studies have shown neuronal subtype-specific molecular and pathological signatures, yet the underlying metabolic shifts driving this selective vulnerability are not completely understood. Here we present iNeuron-GEM, the first manually curated, genome-scale metabolic network of human neurons that integrates transcriptomic and metabolic knowledge to resolve subtype-specific metabolic states. By coupling iNeuron-GEM with single nucleus RNA sequencing data from post-mortem human cohort studies, ROSMAP and SEA-AD, we capture neuronal subtype-specific metabolic features and fluxes and identify perturbations in lipid and energy metabolism across excitatory and inhibitory neurons. Integrative analysis with NPS-AD data shows overlapping metabolic disruptions in AD and schizophrenia (SCZ), suggesting shared molecular vulnerabilities between neurodegenerative and neuropsychiatric disorders. We also developed a computational pipeline to infer transcriptional regulation of metabolic pathways and identify NR6A1 and NR3C1 as important regulators of lipid dysregulation in AD neurons. Our study establishes iNeuron-GEM as a framework to identify neuronal subtype-specific metabolic vulnerabilities in complex brain disorders.

systems biology↗

bioRxiv2025

Differentially acetylated chitosan oligosaccharides as plant defense elicitors against spider mites

The increasing challenges of pesticide resistance and environmental degradation in modern agriculture require sustainable pest management strategies. This study investigates the efficacy of a specific type of hetero-chitooligosaccharide called DACOS, as a plant defense inducer against the two-spotted spider mite, Tetranychus urticae Koch. DACOS is characterized with 85% deacetylation and an average molecular weight of 1 kDa. In planta bioassays revealed a dose-dependent suppression of mite performance on DACOS-treated leaves of kidney bean seedlings, with peak efficacy occurring at 80 ppm. This concentration reduced mite survival by 30% and fecundity by 59% after six days. In addition to the local effects, mite survival and fecundity were also reduced on untreated leaves of the same seedlings, confirming that the effect of DACOS on plant defense is systemic. Behavioral choice assays revealed that DACOS-treated leaves induced 73% mite repellency. No direct acaricidal effects were observed, which confirms the role of DACOS as a plant defense elicitor. Metabolic profiling revealed enriched pathways (e.g., monoterpenoid biosynthesis and -linolenic acid metabolism) that produce volatile organic compounds with repellent properties. These findings suggest that DACOS is an environmentally friendly biostimulant that can enhance plant defense, bypass pesticide resistance, and promote the sustainability of crop production.

physiology↗

bioRxiv2025

Optic nerve regeneration requires the intracellular domain of LIFRa/CD118

Identifying cell-autonomous and non-autonomous factors that govern retinal ganglion cells (RGCs) ability to extend axons is an important step in developing therapies to achieve recovery after optic nerve injury. Here we report that the intracellular domain of the leukemia inhibitory factor receptor (LIFR/CD118) is essential for mature RGCs ability to regenerate injured axons independent of the cognate ligand (LIF) and other therapies. Overexpression of LIFR in adult RGCs induces neurite outgrowth in cultured RGCs and axon regeneration in vivo while strongly amplifying RGCs response to LIF itself and to unrelated growth factors. Conversely, in loss-of-function studies, down-regulation of LIFR eliminates the pro-regenerative effects of Pten deletion and other potent stimuli. LIFR bidirectionally regulates the constitutive activity of the MAP kinase pathway, in contrast to LIF itself, which primarily activates pSTAT3. Expression of a truncated LIFR lacking the extracellular domain is sufficient to promote axon regeneration and selectively increases the survival of particular RGC subtypes, placing the LIFR intracellular domain as an essential, cell-autonomous regulator of optic nerve regeneration.

neuroscience↗

bioRxiv2025

Single-nucleus transcriptomics reveal disrupted pathways in the prefrontal cortex of Scn2a-deficient mice

Truncating variants in SCN2A, which encodes the NaV1.2 sodium channel critical for action potential initiation and propagation, are associated with autism spectrum disorder (ASD) and epilepsy. To investigate SCN2A deficiency-related phenotypes, we developed a preclinical mouse model with under 50% NaV1.2 expression, exhibiting neuronal hyperexcitability and social deficits. However, the neuronal populations and molecular alterations underlying these phenotypes at single-cell resolution have not been investigated. In this study, we conducted single-nucleus RNA sequencing (snRNA-seq) of wild-type (WT), homozygous Scn2a-deficient (HOM) mice, and HOM mice with Scn2a restoration (HOM-FlpO) to examine the effects of Scn2a level on gene expression in the medial prefrontal cortex (mPFC), a critical brain region related to ASD development. Differential expression analysis in GABAergic and glutamatergic neurons between genotypes revealed gene expression enriched in neurotransmitter activity regulation and synapse organization. Lastly, snRNA-seq results in HOM-FlpO identified genes that were rescued after Scn2a restoration. These results reveal that reduced Scn2a expression disrupts RNA transcriptomes in multiple neuronal subtypes, providing insight into cell type-specific mechanisms underlying SCN2A-related disorders.

neuroscience↗

bioRxiv2025

Application of evolutionary algorithms to optimization of Boolean models in biomedicine

Biological processes in health and disease are regulated in great complexity, imposing significant challenges in understanding and modifying their behavior for healthcare applications. Boolean networks have become essential tools for modeling gene regulatory systems and understanding cellular decision-making processes, but their optimization for biological relevance and precision medicine remains challenging. This study presents a comprehensive benchmark comparison of four prominent Boolean network optimization methods involving genetic algorithms, integer linear programming, and answer set programming, evaluating their performance across structural robustness, method reliability, and biological relevance using mean squared error (MSE) as the primary optimization criterion. Through systematic analysis of network reconstruction under varying perturbation levels (10-90%), we demonstrate that each method exhibits distinct performance profiles: answer set programming (ASP) achieves optimal topological similarity with computational efficiency, integer linear programming (ILP) produces reasonable MSE minimization but with high variance, genetic algorithms (GA) shows superior functional reconstruction stability despite longer computational times. Our results reveal critical limitations in current evaluation approaches, particularly the insufficient discriminatory power of F1 scores and Hamming distance metrics, and highlight fundamental trade-offs between data fitting accuracy and topological preservation. The analysis demonstrates that no single optimization method dominates across all criteria, with all methods showing significant performance degradation at perturbation thresholds above 10-30%, suggesting that method selection should be application-specific and guided by requirements for computational efficiency, reconstruction accuracy, and robustness to uncertainty in prior knowledge.

systems biology↗

bioRxiv2025

Human Dermal Fibroblast-derived Spheroids Demonstrate Efficacious Immune Modulation in a Psoriasis Mouse Model

BackgroundPsoriasis is a chronic inflammatory disease associated with high morbidity and few cases of sustained remission. Innovative immunomodulatory therapies, including fibroblast-based cell therapies, offer promising alternatives. This study investigates the therapeutic potential of human dermal fibroblasts (HDFs) organized into three-dimensional (3D) spheroids in a mouse model of imiquimod (IMQ)-induced psoriasis. MethodsHDF spheroids were cultured using Elplasia(R) microcavity plates, and their size, viability, and phenotype were compared with single cells in 2D monolayer cultures. Cellular responses in whole blood and acute inflammatory responses were evaluated at various time points following intravenous injection of HDFs. The therapeutic efficacy of HDF spheroids was assessed using an IMQ-induced psoriasis mouse model, with disease severity scored using the Psoriasis Area and Severity Index (PASI). Optimized HDF spheroids ([~]150 {micro}m, 1x106 cells/mouse) were administered intravenously in a single dose for mild psoriasis or multiple doses for moderate-to-severe psoriasis. The efficacy of HDF spheroids was compared to a pre-clinical monoclonal antibody targeting interleukin 23 (anti-IL-23). ResultsSpheroid cultures of HDFs showed reduced cell size, enhanced viability, and distinct phenotypic changes compared to monolayer cultures. Intravenous injection of HDF spheroids resulted in less thrombocytopenia and reduced acute inflammatory responses compared to single-cell injection. A single dose of HDF spheroids reduced the severity of mild psoriasis by 35%, while repeated doses resulted in a 36% reduction in moderate-to-severe psoriasis. Single-dose administration normalized blood cell counts, alleviated spleen enlargement, and improved cytokine dysregulation. Although HDF spheroids and anti-IL-23 reduced epidermal thickening and immune cell infiltration, HDF spheroids uniquely inhibited monocyte production and infiltration, a benefit not observed with anti-IL-23. No acute or chronic toxicity was observed. ConclusionsHDF spheroids offer comparable therapeutic efficacy to anti-IL-23 in treating psoriasis, with a distinct mechanism involving inhibiting monocyte production and infiltration. Their safety profile and broader immunomodulatory potential support their development as a novel therapeutic strategy for psoriasis and other inflammatory diseases.

immunology↗

bioRxiv2025

Nuclear 2'-O-methylation regulates RNA splicing through its binding protein FUBP1

2'-O-methylation (Nm) is an abundant RNA modification exists on different mammalian RNA species. However, potential Nm recognition by proteins has not been extensively explored. Here, we employed RNA affinity purification followed by mass spectrometry to identify Nm-binding proteins. The candidates exhibit enriched binding at known Nm sites. Interestingly, some candidates display nuclear localization and functions. We focused on the splicing factor FUBP1. Electrophoretic mobility shift assay (EMSA) validated preference of FUBP1 to Nm-modified RNA. As FUBP1 predominantly binds intronic regions, we profiled Nm sites in chromatin-associated RNA (caRNA) and found Nm enrichment within introns. Depletion of Nm led to increased exon skipping, suggesting Nm-dependent splicing regulation. The caRNA Nm sites overlap with FUBP1 binding sites, and Nm depletion reduced FUBP1 occupancy on modified regions. Furthermore, FUBP1 depletion induced exon skipping in Nm-modified genes, supporting its role in mediating Nm-dependent splicing regulation. Overall, our findings identify FUBP1 as an Nm-binding protein and uncover previously unrecognized nuclear functions for RNA Nm modification.

molecular biology↗