Biology subjects

Wang, C.

Publications and source records attributed to Wang, C..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

CANCAN: high-resolution copy number and mutation heterogeneity analysis of DNA sequence data for clinical applications

High-throughput DNA sequencing is central to precision oncology, yet robust and interpretable methods for integrated analysis of copy number alterations and somatic variants across sequencing platforms remain limited. We present CANCAN (Copy number integrative ANalysis in CANcer), a platform-agnostic computational framework for high-resolution analysis of allele-specific copy number and variant data. CANCAN integrates novel normalization and segmentation strategies and enables inference of tumor purity, ploidy, subclonality and mutation multiplicity, while providing statistical confidence estimates and transparent evaluation of alternative solutions. Benchmarking across whole-genome, whole-exome and targeted sequencing datasets from TCGA and the IMPRESS-Norway study demonstrates high concordance with established methods, with particularly strong performance on targeted sequencing data. CANCAN accurately estimates global genomic features, including purity and ploidy, even at reduced sequencing coverage, and shows comparable or improved agreement relative to existing tools. In addition, it provides detailed visualization of the genomic context of clinically relevant biomarkers, supporting diagnostic interpretation. CANCAN constitutes a reproducible and interpretable approach for integrated genomic analysis, addressing key methodological and practical challenges in clinical cancer genomics.

bioinformatics↗

bioRxiv2026

Genetic canalization of nutrient resorption: evidence from a widespread grass under effective salt stress

Nutrient resorption is a key plant strategy for nutrient conservation, yet whether it responds plastically to non-nutrient stressors such as salinity remains unresolved. Using a common garden experiment with 110 genotypes of the cosmopolitan grass Phragmites australis, we first established that the imposed salinity treatment induced strong multi-level stress responses: above-ground biomass declined by >60%, sodium accumulated 3- to 5-fold across all leaf stages, and 484 metabolites showed significant differential accumulation, including canonical markers of osmotic and oxidative stress. Against this backdrop of confirmed stress, we found that nutrient resorption efficiency (NuRE) remained largely unaffected by salinity. Instead, NuRE was strongly correlated with phylogeographic lineage, ecotype, and latitude of origin, demonstrating evolutionary canalization rather than short-term acclimation. Element-specific regulatory patterns were also evident: while phosphorus resorption followed concentration-dependent control regardless of stress, nitrogen control was disrupted under salinity, and potassium resorption showed no such dependence. Our findings reveal that intraspecific variation in nutrient resorption is predominantly shaped by historical adaptation and geographic context, not by plasticity to salinity. This genetic canalization of a key functional trait implies that predictions of nutrient cycling under global change must account for the phylogeographic composition of plant populations.

ecology↗

bioRxiv2026

Astrocytic D1 Dopamine-Signaling Regulates Synaptic Remodeling and Cocaine Seeking

D1-type receptor (D1R)-mediated dopaminergic signaling within the nucleus accumbens shell (NAcSh) is essential for forming adaptive circuit changes that embed persistent memories associated with drug seeking and craving. While D1R is expressed in both NAcSh neurons and astrocytes, the specific contribution of astrocytic D1R to drug-related circuit plasticity remains poorly understood. Here, we demonstrate in mouse NAcSh slices that D1R agonists increase astrocytic Ca2+ activity, an effect that is attenuated by astrocyte-specific D1R knockdown. Furthermore, selective knockdown of astrocytic D1R in the NAcSh prior to cocaine self-administration inhibits cocaine-induced generation of silent synapses, therefore hampering the associated remodeling of NAcSh circuits. Behaviorally, knockdown of NAcSh astrocytic D1R expedites the extinction of cocaine seeking and reduces cue-induced reinstatement. These results identify astrocytic D1R as a fundamental component of NAcSh dopamine signaling during cocaine experience that remodels synaptic connections and neural networks underlying drug seeking and relapse.

neuroscience↗

bioRxiv2026

An Engineered Halotolerant Chimeric T7 RNA Polymerase for High-Yield, Low-Immunogenicity Synthesis of RNA via Simple Batch Transcription

The rapid advancement of mRNA therapeutics has imposed stringent requirements on both the quality and scalability of in vitro transcription (IVT) products. However, the accumulation of double-stranded RNA (dsRNA) byproducts and 3-terminal heterogeneity during T7 RNA polymerase (T7 RNAP)-mediated transcription can robustly trigger deleterious innate immune responses and compromise translation efficiency. Existing enzyme engineering strategies frequently struggle to reconcile the trade-offs between salt tolerance, volumetric productivity, and product purity. Here, we report a novel engineering strategy for halotolerant T7 RNAP by fusing optimized mutant polymerases with diverse DNA-binding domains (e.g., Sso7d, MC1). This approach orchestrated the development of a series of chimeric T7 RNAP mutants designed to bolster catalytic activity and template selectivity under high-salt conditions while concurrently suppressing RNA-dependent RNA polymerase (RdRP) activity. Our lead chimeric mutants exhibited exceptional salt tolerance and processivity in the presence of up to 270 mM NaCl. Notably, these mutants significantly diminished dsRNA formation to less than 0.001%, while markedly improving transcript integrity and 3 homogeneity, thereby facilitating superior translation efficiency for both linear mRNA and circular RNA (circRNA). Crucially, this heightened salt tolerance does not necessitate a trade-off in RNA yield, affording broader flexibility for downstream process optimization. In an enzymatic circRNA synthesis system, these mutants enabled a non-fed-batch configuration with high initial rNTP concentrations (15 mM each), resulting in a 50% increase in yield and achieving an unprecedented titer of 15 mg/mL. This research provides a robust enzymological solution that harmonizes quality and productivity for the industrial-scale manufacturing of high-concentration, low-immunogenicity RNA.

genomics↗

bioRxiv2026

IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches

Integrating single-cell and spatial transcriptomics data across batches is essential for recovering comparable cell identities--including cell types, subtypes, and states--as a prerequisite for downstream analyses in multi-condition and large-scale studies. This task remains challenging because between-batch variation removal often conflicts with cell identity preservation, and current methods typically rely on generic highly variable gene selection and lack principled metrics for hyperparameter tuning when cell identity annotations are unavailable. Together, these limitations often lead to over-integration, which merges biologically distinct cell identities, or under-integration, which leaves cells separated by batch rather than identity. Here we introduce IntegrateRigor, a data-driven, annotation-free, method-agnostic framework that optimizes integration specifically for reliable cell identity recovery across batches. IntegrateRigor first selects genes whose expression patterns are stable across batches using a gene-wise likelihood-based batch stability score, excluding batch-sensitive genes that can bias cell identity alignment during integration. It then identifies the optimal integration configuration across methods and hyperparameters by defining a dataset-level integration score that explicitly balances between-batch variation removal against cell identity preservation, without requiring prior annotations. In a colorectal cancer single-cell and spatial transcriptomics dataset, IntegrateRigor revealed previously uncharacterized cancer-immune interface niches in the tumor microenvironment that were masked by under-integration under default settings and by over-integration in previous literature. Across diverse datasets spanning multiple sources of between-batch variation, IntegrateRigor consistently improved cell identity recovery by mitigating both over-integration and under-integration across five state-of-the-art integration methods. By transforming integration from a heuristic preprocessing step into a statistically principled, dataset-adaptive procedure for cell identity recovery, IntegrateRigor improves the reproducibility and biological discovery power of large-scale single-cell and spatial transcriptomics analyses.

bioinformatics↗

bioRxiv2026

Structural Basis of Ligand-Specific Orthosteric-Allosteric Coupling and Sensory Tuning in the Human Bitter Taste Receptor TAS2R14

The bitter taste receptor TAS2R14 recognizes hundreds of structurally diverse ligands, yet the mechanisms governing its broad promiscuity, graded agonist efficacy, and multi-site regulation remain unclear. Here, we report cryo-EM structures of TAS2R14-Gi1 complexes bound to 3,5-diiodosalicylic acid (DA), flufenamic acid (FA) and aristolochic acid (AA) at resolutions of 2.44 [A], 2.39 [A], and 2.69 [A], with a clear efficacy hierarchy of AA > FA > DA. Transmembrane helix 6 (TM6) acts as a core regulatory hub, with agonist binding triggering 12 [A] lever-like TM6 rearrangements to reshape receptor interfaces and modulate G-protein coupling strength. We also identify cholesterol hemisuccinate (CHS) as a new TAS2R14 orthosteric agonist, selectively potentiating DA-mediated signaling potency by [~]5-fold via allosteric-orthosteric coupling without affecting FA or AA. Our findings show TM6 dynamics unify TAS2R14s key functional features, advancing insights into bitter receptor activation and sterol regulation.

molecular biology↗

bioRxiv2026

A Panel of Human Monoclonal Antibodies for Tracking the Antigenic Evolution of Influenza H5N1 Clade 2.3.4.4b

The ongoing panzootic of clade 2.3.4.4b H5N1 influenza has resulted in widespread infection of birds, mammals, and livestock, underscoring the need for tools to interpret its real-time evolution. Here, we describe the isolation and characterization of a panel of 19 human monoclonal antibodies that potently neutralize current isolates. Competition immunoassays and cryo-electron microscopy analyses revealed their collective near-complete epitope coverage of the H5-hemagglutinin surface. Neutralization profiling across multiple historical and contemporary H5 viruses defined their epitope-specific patterns of virus neutralization. One cluster of antibodies potently neutralized only clade 2.3.4.4b viruses, while many others exhibited broadly neutralizing activity against diverse H5N1 clades. Application of this structurally calibrated antibody panel to recent North American human isolates revealed genotype-specific antigenic divergence between lineages that have spread among cattle (B3.13) and poultry (D1.1). Together, the findings of this study establish a structurally grounded antibody reference panel spanning major vulnerable sites of H5 hemagglutinin and provide a toolbox for interpreting emergent mutations, monitoring ongoing antigenic drift, and anticipating the evolutionary trajectory of circulating H5N1 influenza viruses.

microbiology↗

bioRxiv2026

Collagen targeting IL-12 combined with Doxorubicin enhances the anti-tumor effect against osteosarcoma

Osteosarcoma (OS) is the most prevalent primary bone malignancy in children and adolescents; however, therapeutic outcomes remain suboptimal due to tumor heterogeneity, chemoresistance, and inadequate immune activation. Doxorubicin (Dox), the standard therapy that induces immunogenic cell death, has its efficacy compromised by the immunosuppressive tumor microenvironment (TME). While interleukin-12 (IL-12) can activate and recruit various immune cells, making it an attractive combination partner, its systemic delivery is severely limited by dose-limiting toxicity. We have previously reported that intravenous injection of A3 collagen binding domain (CBD) of von Willebrand Factor preferentially accumulates into the TME of various tumor models enriched in collagen I and III. Furthermore, CBD-fused IL-12 (CBD-IL-12) demonstrated superior therapeutic effects against various cancer models compared to unmodified IL-12 due to its collagen-targeted delivery and the resulting tumor-localized inflammation. Given that the OS TME also exhibits higher collagen I and III expression compared to normal bone, we hypothesized that a CBD-IL-12 fusion protein could showcase potent anti-tumor efficacy in OS via tumor-specific accumulation. Here, we demonstrated that CBD-IL-12 exhibited 4-fold enhanced tumor accumulation compared to unmodified IL-12 and increased cytotoxic T cell infiltration by 2.2-fold within the immune-cold microenvironment in a mouse model of OS. The combination of CBD-IL-12 with Dox significantly prolonged median survival in two independent murine OS models. This coordinated approach utilizing Dox coupled with precision-targeted IL-12 immunotherapy represents a clinically translatable strategy that overcomes the inherent limitations of single-agent treatments for OS. HighlightO_LICollagen-targeted IL-12 increases tumor accumulation in osteosarcoma. C_LIO_LIThe collagen-targeted IL-12 synergizes with doxorubicin in osteosarcoma models. C_LIO_LICombination therapy enhances T cell differentiation and activates innate immunity. C_LI

bioengineering↗

bioRxiv2026

SigBridgeR: An Integrative Framework and Toolkit for Comprehensive Screening and Benchmarking of Phenotype-Associated Cell Subpopulations in Single-Cell Transcriptomics

Single-cell RNA sequencing has revolutionized our understanding of cellular heterogeneity, yet linking specific cell subpopulations to clinically relevant phenotypes remains a persistent challenge. Although multiple computational methods have been developed to bridge this gap, they are typically implemented as standalone packages with heterogeneous preprocessing pipelines, incompatible parameter conventions, and divergent output formats, thereby hindering rigorous cross-method benchmarking and reproducible multi-method workflows. Here, we present SigBridgeR, an extensible R framework and comprehensive toolkit that currently unifies eight state-of-the-art phenotype-associated cell screening algorithms within consistent workflows. We conducted a systematic benchmarking study across four cancer types HER2-positive breast cancer, triple-negative breast cancer, lung adenocarcinoma, and ovarian cancer using both binary phenotypes and patient survival endpoints. Our evaluation incorporated positive and negative control assessments based on differentially expressed genes and randomly selected marker panels, alongside quantitative accuracy comparisons using ground-truth cell labels. Building upon these insights, SigBridgeR provides standardized preprocessing for scRNA-seq and bulk transcriptomic data, unified algorithmic interfaces through a registry-based architecture, ensemble analysis via weighted voting, and comprehensive visualization utilities for multi-method comparison. By lowering technical barriers and promoting methodological standardization, SigBridgeR facilitates reliable discovery of phenotype-relevant cell subpopulations and enhances the translational potential of single-cell omics research.

bioinformatics↗

bioRxiv2026

MuseDrift: Navigating Protein Evolutionary Manifolds with Conditional Discrete Diffusion

Protein engineering often requires generating variants of a wild-type (WT) sequence while controlling how far they drift in sequence space. Existing generative models support de novo design but offer limited control over WT similarity. We introduce MO_SCPLOWUSEC_SCPLOWDO_SCPLOWRIFTC_SCPLOW, a conditional discrete diffusion model for WT-anchored, distance-controlled protein generation. Trained on a 38.2M-pair Seed-and-Stratify corpus, MO_SCPLOWUSEC_SCPLOWDO_SCPLOWRIFTC_SCPLOW combines WT-prefix conditioning with random-order iterative unmasking to enable stable multi-residue generation. Its key feature is a calibrated identity dial: after lightweight calibration, generated sequences match a target WT identity{tau} within approximately {+/-}0.05 over{tau} [isin] [0.55, 0.95] on held-out probes. On Mol-Instructions and CAMEO under shared evaluation oracles, MO_SCPLOWUSEC_SCPLOWDO_SCPLOWRIFTC_SCPLOW is competitive with multimodal and text-conditioned baselines while uniquely providing explicit identity control. At{tau} = 0.95, it achieves pLDDT scores of 84.97 on Mol-Instructions and 83.14 on CAMEO with only 85M parameters, rivaling much larger 1.8B-2B models. Evolutionary and FO_SCPLOWOLDC_SCPLOWX analyses further support biological plausibility and structural stability.

bioinformatics↗

bioRxiv2026

Histone modifications analysis reveals enhancers reprogramming during maternal-to-zygotic transition

Enhancers are important epigenetic regulatory components that coordinate spatiotemporal gene expression and play a crucial role in mammalian development, gene regulation, and illness. During early mammalian embryogenesis, histone modifications including H3K4me1, a canonical enhancer mark, and H3K27ac, which identifies active enhancers, are still poorly understood. This study profiles the genome-wide H3K4me1 and H3K27ac patterns in mouse oocytes and pre-implantation embryos using low-input CUT&RUN (cleavage under targets and release using nuclease) with input as low as 50 cells. Both markers are enriched in distal regions and exhibit distinct sequence preferences and reprogramming dynamics in pre-implantation embryos. H3K27ac, a mark of active enhancers, is reprogrammed at the 2-cell stage, whereas H3K4me1 is remodeled at the 4-cell stage and overlaps with H3K27ac, coinciding with accessible chromatin regions. Interestingly, H3K4me1 and H3K27ac are co-localized in promoter regions, where they are mutually exclusive to H3K4me3. Enhancers are dynamically remodeled during maternal-to-zygotic transition (MZT). there are three enhancer types: active enhancers (H3K4me1/H3K27ac), primed enhancers (H3K4me1), and poised enhancers (H3K4me1/H3K27me3). Active enhancers increase significantly after zygotic genome activation. Further, super-enhancers are present across the genome and are mainly enriched in promoters. The specific motifs enriched by super-enhancers may be associated with the variations of gene expressions at different stages.

developmental biology↗

bioRxiv2026

scLASER: a robust framework for simulating and detecting time-dependent single-cell dynamics in longitudinal studies

Longitudinal single-cell clinical studies enable tracking within-individual cellular dynamics, but methods for modeling temporal phenotypic changes and estimating power remain limited. We present scLASER, a framework detecting time-dependent cellular neighborhood dynamics and simulating longitudinal single-cell datasets for power estimation. Across benchmark experiments, scLASER shows consistently higher sensitivity than traditional cluster--based approaches, with particularly pronounced gains in rare cell types and non-linear temporal patterns. Applications to inflammatory bowel disease (95,813 cells, 38 patients) reveal treatment-responsive NOTCH3+ stromal trajectories with high cell type discrimination (AUC > 0.92), while analysis of COVID-19 data (188,181 cells, 84 patients) identifies three distinct axes of T cell activity (cytotoxic effector, NK immunoreceptor signaling, and interferon-stimulated gene programs) over disease progression. scLASER enables robust longitudinal single-cell analysis and optimization of study design. TeaserA new framework detects time-dependent cellular dynamics and enables power estimation for longitudinal clinical single-cell studies.

bioinformatics↗

bioRxiv2026

Reh1 is Required for Nonfunctional 25S RNA Decay

25S nonfunctional RNA decay (NRD) eliminates 60S ribosomal subunits carrying inactivating mutations in the RNA. However, how cells identify defective subunits has not been described. We recently showed that the zinc-finger protein Reh1 is the last assembly factor to be released from a nascent 60S subunit. We now show that in yeast Reh1 is required for the degradation of 25S NRD substrates. 25S rRNAs carrying mutations in the catalytic center, A2820G or U2954A (A2451 and U2585, respectively in E coli numbering), are unstable in wildtype cells but are fully stabilized when REH1 is deleted. However, not all 25S rRNA mutations are recognized by Reh1. Ribosomes with a truncated L1 stalk engage in translation but cannot support viability. These ribosomes display a half-life indistinguishable from wild-type rRNA, suggesting that yeast does not have a robust surveillance system for such mutant ribosomes. Deletion of REH1 also has no impact on the levels of defective 18S rRNA. These results indicate that Reh1 and 25S NRD are specific for mutations in or near the catalytic center of the ribosome.

molecular biology↗

bioRxiv2026

Striatal FOXP2 is essential for stable vocal production in non-human primates

The transcription factor FOXP2 is the most well-known language-related gene in humans, yet its role in primate vocalization remains poorly understood. Here we report that knockdown of FOXP2 in the striatum markedly disrupts vocalization stability in the marmoset monkey, a valuable non-human primate model for studying vocal behavior. FOXP2 exhibited high expression in the marmoset striatum, especially during early development. Using the CRISPR-Cas12 system, we achieved specific in vivo editing of the FOXP2 gene and effective knockdown of FOXP2 protein expression in the marmoset striatum. Two neonatal marmosets received bilateral striatal injections of the gene-editing and control virus, respectively, and were raised together in the same family. In three such marmoset pairs, analysis of vocalizations recorded during 6-15 weeks post-injection revealed that striatal FOXP2 knockdown significantly altered vocal features and increased intra-individual variability in phee syllables--the most common marmoset vocalization, often produced repetitively as multi-syllable phee calls. Notably, in FOXP2-edited marmosets, acoustic alterations were minimal in the first syllable of phee calls but became progressively more pronounced in subsequent syllables, which exhibited a marked upward shift in the frequency spectrum over time with progressively steeper slopes. These temporal dynamics in vocal features reflect a reduction in the stability of continuous vocal production. In line with the known striatal functions in motor control, our findings provide the first evidence of FOXP2 in controlling vocalization in non-human primates, thereby opening new avenues for investigating the neural mechanisms underlying FOXP2 function.

neuroscience↗

bioRxiv2026

SpatialBench: Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue

Spatial transcriptomics (ST) has rapidly expanded with the introduction of multiple high-resolution platforms, yet cross-platform benchmarking remains limited and largely focused on technical performance. Here we present SpatialBench, a matched multi-platform resource comprising Visium HD, Xenium and MERSCOPE data together with single-cell and single-nucleus references from a malaria-challenged wild-type and B cell-specific Tbx21 knockout mouse spleen model. In this system, loss of T-bet in B cells disrupts germinal center (GC) polarization and antibody maturation, providing a biologically grounded benchmark for technology comparison. We leveraged this system to systematically evaluate ST platform performance using technical and biological readouts. Across platforms, immune organization and Tbx21-associated programs were consistently recovered, indicating robustness of major biological signals. Platforms instead differed in the level of biological resolution accessible. Visium HD enabled transcriptome-scale GC characterization and, together with Xenium, resolved dark and light zone organization, whereas GC zonation was not resolved in MERSCOPE, consistent with differences in transcript detection sensitivity. SpatialBench provides a biologically defined reference dataset for evaluation of ST technologies, method development, computational benchmarking, and studies of GC spatial organization in lymphoid tissue.

bioinformatics↗

bioRxiv2026

TORC1 spatial segregation and hysteresis are regulated by the small GTPase Arf1

TORC1 is a central regulator of growth, integrating inputs from kinases and signaling proteins. How TORC1 activity is regulated, is still not completely understood. The small GTPase Arf1 has been implicated in TORC1 regulation, but the underlying mechanism remains elusive. Here, we show that Arf1 controls TORC1 in an allele-specific manner under nutrient and heat stress in yeast. Unexpectedly, both the hyperactive mutant arf1-11 and the loss-of-function mutant arf1-18 reduce TORC1 activity, while other loss-of-function alleles did not. We reveal two distinct functions of Arf1: first, it ensures Golgi-to-vacuole/lysosome transport for the functional maintenance of these organelles; second, it regulates TORC1 activity at the ER-Golgi-vacuole interface. Hyperactive Arf1-11 drives sequestration of Kog1 and Tor1 into cytoplasmic foci, to which Arf1-11 can be equally recruited. Importantly, Arf1 also promotes TORC1 re-activation during stress recovery - so-called hysteresis. Our data reveal an unexpected dual function for Arf1 as a negative and a positive regulator of TORC1 activity in a context-dependent manner. TeaserThe small GPTase Arf1 acts as a dual switch for the key cellular growth regulator TORC1 by increasing or decreasing TORC1 activity depending on nutritional status and stress.

cell biology↗

bioRxiv2026

A High-Fidelity 3D Fluid-Structure Interaction Framework for Predictive Microfluidic Design

The commercial maturation of microfluidics remains bottlenecked by empirical prototyping and an absence of predictive digital design capabilities. Because optimizing advanced technologies such as passive particle separation fundamentally hinges on the precise coupling of fluid dynamics and particle mechanics, conventional two-dimensional or decoupled fluid simulations inherently fail to capture authentic multiscale behaviors. To bridge this gap, we establish a high-fidelity three-dimensional fluid-structure interaction framework combining a high-order Arbitrary Lagrangian-Eulerian mapping-based finite element method with a localized hierarchical dynamic mesh strategy. Engineered to accurately resolve complex multiscale hydrodynamics, this architecture utilizes deterministic lateral displacement structures as a stringent test case. Validated against experimental data for rigid microspheres and tumor cells, the framework predicts transport trajectories and critical separation diameters with sub-micron precision. Crucially, the simulation explicitly resolves the M-shaped spatial fluctuation of local size thresholds alongside the dynamic vertical migration of particles. Unveiling these hidden physical mechanisms provides a deterministic explanation for highly debated phenomena such as mixed-mode transport. By enabling the rigorous in silico evaluation of complex non-periodic architectures, this framework serves as a powerful instrument for predictive structural optimization. Such capabilities establish the essential infrastructure for microfluidic digital design, accelerating the transition from empirical trial-and-error to precision simulation-driven engineering.

bioengineering↗

bioRxiv2026

Systems Pharmacology Reveals Type I Interferon and Myeloid-Like B Cell Reprogramming as Druggable Axes in Antiphospholipid Syndrome

Antiphospholipid syndrome (APS) lacks targeted therapies beyond anticoagulation, and its molecular heterogeneity remains poorly characterized. We employed an integrative systems pharmacology approach combining weighted gene co-expression network analysis (WGCNA), single-cell RNA sequencing, Connectivity Map (CMap) screening, and molecular docking to identify druggable targets in APS. WGCNA of bulk RNA-seq data from neutrophils (n = 18) and whole blood (n = 88) identified two disease-associated modules: ME10 (176 genes, r = 0.77, interferon-I signaling) and ME2 (3409 genes, r = 0.79, degranulation/innate activation). Single-cell analysis of 26,936 B cells revealed transitional B cells with elevated ME2 scores and aberrant SPI1 expression, suggesting myeloid-like transcriptional reprogramming. CMap analysis ranked chloroquine, a first-line APS therapy, among top ME2 candidates (NCS = -2.07), validating the computational approach. DrugBank mapping identified 14 FDA-approved drugs targeting module genes, and a 3-gene machine learning signature (CORO1A, ANKRD22, IFITM1) achieved cross-tissue validation AUC of 0.802. External validation confirmed ME2 pathway modulation by NAPc2 intervention and cross-tissue module conservation in platelets. Patient-level ME10 x ME2 stratification revealed four molecular subtypes with distinct pathway activation profiles. This framework nominates druggable targets across both IFN-I and degranulation pathways, providing a foundation for pathway-guided precision medicine in APS.

bioinformatics↗