Biology subjects

Wang, M.

Publications and source records attributed to Wang, M..

At least 145 records · Page 8Linked to original sources

bioRxiv2026

Healthcare Infrastructure Shapes Evolutionary Trade-offs and Geographic Dissemination of Multidrug-Resistant Acinetobacter baumannii

Antimicrobial-resistant pathogens pose an existential threat to modern medicine, yet the evolutionary forces driving their adaptation in healthcare systems remain largely unexplored. We revealed that hospital network architecture functions as a primary selective pressure, driving pathogen evolution through infrastructure-dependent virulence-transmission trade-offs. Phylogenomic analysis of 5,023 Acinetobacter baumannii isolates across Chinas centralized healthcare system identifies two co-existing evolutionary strategies: a virulence-optimized clade (ESL2.4) that spread slowly (20.4 km per year) in low-connectivity hospitals, and a transmission-optimized clade (ESL2.5) that disseminate rapidly (65.2 km per year) through mega-city healthcare hubs, likely attributed to its capsule conversion and increased upper respiratory colonization. Comparative analysis with European A. baumannii populations demonstrates that healthcare connectivity, not geography, governs pathogen distribution through convergent genomic adaptations. Our simulation suggests competitive asymmetries of the two clades, following the ecotype principle and enabling stable coexistence. The COVID-19 pandemic provided a natural experiment validating these mechanisms: outpatient restrictions reduced transmission-optimized lineage spread by 89%, while virulence-optimized lineage persisted through inpatient networks. These findings establish healthcare infrastructure as a critical evolutionary driver with immediate implications for predicting and controlling antimicrobial resistance emergence across diverse healthcare systems.

microbiology↗

bioRxiv2026

Genome-wide investigation of WRKY gene family in Lagenaria siceraria

BackgroundA significant family of transcription factors known as WRKY genes include many physiological functions and environmental adaptations. However, insufficient information was previously available about the WRKY genes in Lagenaria siceraria, a crucial crop with substantial economic significance. The recent publication of the whole-genome sequence of L. siceraria has allowed us to perform a genome-wide investigation of the organization of the WRKY genes in L. siceraria. ResultsIn the present study, 57 L. siceraria WRKY (LsiWRKY) genes were identified and given new names based on their relative chromosomal distribution. The 57 LsiWRKYs were further divided into three major groups and several subgroups based on their structural and phylogenetic properties. Segmentation duplication events have played a major role in the expansion of the WRKY gene family in L. siceraria. Phylogenetic comparisons of the Group III WRKY genes provide valuable insights into the evolutionary characteristics of WRKY genes in L. siceraria. Additionally, RNA-seq analysis revealed distinct expression pattern of WRKY genes across different tissues. ConclusionsThis study presents a preliminary analysis of the WRKY gene family in L. siceraria, including their structural characteristics, evolutionary traits, and tissue-specific expression patterns. The systematic insights provided here serve as a foundation for further functional studies aimed at enhancing L. siceraria crops. This knowledge holds promise for improving the cultivation and yield of L. siceraria, thereby contributing to agricultural advancements.

genomics↗

bioRxiv2025

Theta-Band Temporal Interference Stimulation of the Dorsal Anterior Cingulate Cortex Enhances Prediction Error Processing in Individuals With Food Addiction

BackgroundPrediction error (PE) signals encode discrepancies between expected and actual outcomes and are linked to medial frontal theta dynamics in the dorsal anterior cingulate cortex (dACC). However, causal evidence that dACC theta mechanisms contribute to PE gain in humans remains limited. Transcranial temporal interference stimulation (tTIS) enables non-invasive modulation of deep cortical targets and provides a strategy to probe dACC theta circuitry. ObjectiveTo determine whether theta-band tTIS targeting the dACC modulates the neural gain of prediction error encoding during reward processing. MethodsThirty-four participants with elevated food addiction-related symptoms were randomized in a single-blind, sham-controlled pre-post design to active theta-band tTIS or sham stimulation. Under satiety, participants completed a food incentive delay task while EEG was recorded before and after stimulation. Feedback-related negativity (FRN) was analyzed at mean and single-trial levels using mixed-effects models with behavioral and Rescorla-Wagner model-derived prediction errors. Stimulus-preceding negativity (SPN) indexed anticipatory processing. ResultsTheta-band tTIS selectively modulated feedback-stage prediction error encoding. It altered the trial-level FRN-prediction error slope, with pre-to-post changes differing between groups for both behavioral ({beta} = 1.74, p = .049) and model-derived prediction errors ({beta} = 1.77, p = .048). At the mean ERP level, FRN became more negative after active stimulation (t16 = 2.75, p = .014), whereas SPN was unaffected. ConclusionTheta-band tTIS targeting the dACC modulates neural sensitivity to prediction errors during reward feedback, providing causal evidence that medial frontal theta dynamics regulate the neural gain of prediction error encoding.

neuroscience↗

bioRxiv2025

Mitochondrial ROS-induced metabolic alterations differentially regulate ferroptosis sensitivity

Ferroptosis is an iron-catalyzed lipid peroxidation (LP)-dependent cell death. Induction of mitochondrial ROS (mtROS) is crucial in the execution of ferroptosis, but the underlying mechanism remains unclear. Through utilizing the hepatocyte model and RNA-seq analysis, we determined mtROS-dependent metabolic changes that modulate ferroptosis sensitivity. Elevated mtROS production and LP suppressed glycolysis, fatty acid oxidation, and citric acid cycle activity, representing adaptive responses that protect cells from ferroptosis. On the other hand, mtROS-driven signaling impaired glutathione biosynthesis and downregulated genes involved in coenzyme Q10 (CoQ) biosynthesis, including those in the mevalonate pathway and CoQ8A, a key stabilizer of the CoQ biosynthetic complex. Importantly, silencing CoQ8A expression enhanced, whereas overexpression of CoQ8A reduced, ferroptosis susceptibility of hepatocytes and various cancer cell types. The mtROS-mediated downregulation of CoQ8A was dependent on farnesoid X receptor (FXR) and retinoid X receptors (RXRs). Collectively, our findings highlight that mtROS promotes ferroptosis, at least in part, by suppressing glutathione and CoQ biosynthesis.

cell biology↗

bioRxiv2025

TUPAD: A Tn5-Mediated, Pre-amplification/Adapter-Dimer-Free Platform for Ultra-Uniform, One-Step PGT Profiling with High Stability and Broad Compatibility

High-throughput sequencing stands as a cornerstone of clinical molecular diagnostics, particularly in preimplantation genetic testing (PGT)--a key application where the selection of chromosomally normal embryos is critical to enhancing in vitro fertilization (IVF) success rates. A fundamental challenge inherent to PGT, however, lies in the ultra-low gDNA input (typically <100 pg) from embryo biopsies. To mitigate this limitation, traditional workflows rely on whole genome amplification (WGA) technologies, such as MDA, PicoPlex, and MALBAC. Yet these WGA-based protocols inherently entail pre-amplification of gDNA prior to standard library construction---a step that introduces significant coverage bias and compromised uniformity. These are intrinsic flaws irreparable by downstream library preparation or bioinformatics analysis, ultimately leading to clinical uncertainty in the interpretation of copy number variations (CNVs). In this study, we developed TUPAD (Tn5-Mediated, Uniform Pre-amplification-free and Adapter-Dimer-Free Library preparation), a transformative technology that bypasses the limitations of traditional WGA. By engineering a novel adapter-dimer-free transposon system, TUPAD enables high-efficiency library construction from as little as 1 picogram (pg) of gDNA. This breakthrough allows for a pre-amplification-free workflow, effectively eliminating the primary source of amplification bias. Compared to existing WGA standards, these advantages are fully retained in embryo biopsy and positive sample testing, TUPAD consistently generates highly uniform library data, significantly enhancing the detection limit and accuracy of CNVs and other genomic variants. Beyond these performance advantages, TUPAD also cuts wet-lab processing time by 50%. Practical validation confirms TUPAD results are stable, reliable, with proven practical utility in PGT testing.

molecular biology↗

bioRxiv2025

Mapping Core Components of Membrane-less Organelles in Living Cells by Phase-APEX2 Proximity Labeling

Membrane-less organelles (MLOs), formed via liquid-liquid phase separation, are crucial for organization of biomacromolecules and cellular processes, yet their dynamic nature challenges compositional analysis. Conventional proximity labeling methods lack the specificity to overcome high background and systematic biases inherent in studying these condensates. Here we introduce Phase-APEX2, a three-input AND-gate strategy that dramatically enhances labeling specificity. By integrating a split-APEX2 system with a light-controlled H2O2 generator, we developed Phase-APEX2 platforms for two application contexts: Phase-APEX2-MS for proteomics and Phase-APEX2-seq for genomics. Our analyses revealed not only the core interactomes of the nucleolus and stress granules with high accuracy but also uncovered distinct "molecular grammars" governing their assembly and a surprising link between nucleolar dynamics and the transcriptional regulation of mitosis-related genes. This highly specific and adaptable platform opens new avenues for exploring the composition and function of diverse biomolecular condensates.

cell biology↗

bioRxiv2025

Genetic architecture and evolution of stripe rust resistance uncovered using diverse panels of wheat lines and North American Puccinia striiformis f. sp. tritici isolates

Newly emerging highly virulent races of Puccinia striiformis f. sp. tritici (Pst) often defeat deployed resistance genes (Yr), highlighting the need for novel sources of durable resistance. A global diversity panel of 377 spring wheat (Triticum aestivum L.) lines was screened for all-stage resistance (ASR) against 20 diverse Pst isolates at the seedling stage and adult plant resistance (APR) against natural mix of field races. Genome-wide association mapping identified 77 unique Yr loci. Of these, 33 overlapped with the previously reported ~1,100 loci, while 44 were likely novel. Nine mapped Yr loci were effective at the adult plant stage and showed no overlap with the known APR genes. Two wheat lines, though lacked the widely effective Yr5 and Yr15 genes, exhibited resistance to all 20 Pst races at the seedling stage and natural field races at the adult stage, suggesting that they may carry novel, broad-spectrum resistance alleles. APR genes Yr18, Yr29, and Yr36 were detected at low frequencies, indicating that much of the observed resistance may arise from less characterized or novel sources. Wheat improvement had no effect on the frequency of ASR alleles but resulted in a three-fold increase in the frequency of APR alleles, suggesting that the latter were subjected to more consistent breeding selection over time. Our findings underscore the value of combined screening of diverse germplasm with the diverse panels of pathogen races to identify novel sources of broad-spectrum resistance for breeding stripe rust resistant cultivars.

genetics↗

bioRxiv2025

Ecology of hydrocarbon degradation in widespread viruses

Hydrocarbons are vital for energy production and lead to serious environmental issues due to pollution. Microorganisms largely drive the production and degradation of hydrocarbons, yet little is known about viral contributions to hydrocarbon degradation. Here we identified 786 viral contigs from IMG/VR(v4), encoding five aerobic (alkB, ladA, almA, ndoB and dszC) and three anaerobic (bssA, ebdA and abcA) hydrocarbon-degrading genes (HDGs). vOTUs encoding HDGs span 26 distinct viral families, including 249 are mainly associated with host-associated environment and 463 are derived from aquatic habitat, respectively, implying that these viruses are broadly engaged in hydrocarbon-degradation processes across the entire biosphere. alkB (35%) and almA (28%) was tended to be encoded by Schizomimiviridae, bssA was tended to be encoded by T5-like bacteriophages (29%) and SPO1-like bacteriophages (22%), suggesting that the carriage of HDGs by viruses exhibits taxonomic specificity. With respect to host associations, Pseudomonadota and Bacillota constitute the two main potential host lineages, associated with 268 and 71 vOTUs, respectively. The profiling of ecological footprint reveals that viruses contribute a total of up to 30% gene abundance and 32% transcribing activity to hydrocarbon degradation in the global ocean. This study systematically revealed the distribution, diversity, virus-host correlation and activity of virus-encoded HDGs, underscoring the significant role of viruses in hydrocarbon metabolism on a global scale.

ecology↗

bioRxiv2025

Rapid robust high-fidelity 3D neuronal extraction from multi-view projections

Recent developments in imaging facilitate large-scale three-dimensional (3D) neuronal recording. While these huge amounts of data shed new light on population-level neural coding, it is much harder to extract neuronal calcium dynamics from 3D volumes than 2D images with the existence of noise and scattering. Here, we presented DeepWonder3D, a general end-to- end pipeline for rapid and robust 3D neuronal extraction with high fidelity. Instead of processing voxel by voxel, DeepWonder3D works on the multi-view projections of 3D imaging data obtained either digitally or optically through specific point spread functions (PSFs) for general applicability to diverse techniques, including point-scanning microscopy, light- field microscopy, and two-photon synthetic aperture microscopy. Integrating denoising, resolution registration, background removal, neuronal extraction, and multi-view fusion into a unified pipeline tailored for large-scale high-resolution datasets contaminated by noise and scattering, DeepWonder3D outperforms state-of-the-art methods in 3D localization accuracy with a 10-fold reduction in computational costs, validated by numerical simulations and a hybrid two-photon/light-field imaging system. With the RUSH3D mesoscope, DeepWonder3D achieves rapid high-fidelity 3D calcium extraction of tens of thousands of neurons across the mouse cortex within hours.

neuroscience↗

bioRxiv2025

S1PR3 mediates glial stimulated tumor invasion in response to interstitial fluid flow

Cellular invasion is a primary challenge to complete resection and treatment of glioblastoma, the most aggressive and deadly primary brain tumor. The brain tumor microenvironment actively stimulates glioma invasion through a multitude of cellular, chemical, and biophysical cues. We and others have shown elevated interstitial fluid flow at the tumor border is one such biophysical cue that directly stimulates invasion through tumor-intrinsic signaling and, in other tumor types, priming of cancer-associated stromal cells. It is currently unclear if interstitial flow similarly primes neuroglial cells to promote glioma cell dissemination and can be targeted for therapeutic purposes. Here, we show elevated interstitial flow upregulates expression of sphingosine-1-phosphate receptor 3 (S1PR3) in glial astrocytes and microglia, which drives glioma cell invasion via chemotaxis. Flow-induced expression of glial S1PR3 is tumor-independent and displays a biphasic relationship to fluid shear stress magnitude in vitro and flow rate in vivo. Inhibition of glial S1PR3 in a tissue engineered culture model and orthotopic mouse model abrogates flow-stimulated invasion, demonstrating a tumor-extrinsic approach to limiting glioblastoma progression. Given prior evidence of a pro-inflammatory role for glial S1PR3, identification of S1PR3 as a disease-agnostic marker of flow-stimulated glia may also have therapeutic implications across myriad neuropathologies.

cancer biology↗

bioRxiv2025

The Human Hippocampus Is Involved in Auditory Short-Term Memory Trace Formation

The human hippocampus has been claimed to play an important role in long-term memory, or episodic memory, but its contribution to short-term memory remains debated. Here, we demonstrate human hippocampal involvement in auditory short-term memory (ASTM) trace formation. We used a classic oddball paradigm and intracranial recordings across various human brain areas. High frequency activities evoked by deviant stimuli in subjects indicate the generation of ASTM trace. Analysis of auditory response latencies across the hippocampus, insula, and temporal, parietal, and frontal lobes revealed the early processing of ASTM trace at a pre-attention stage. Granger causality analysis further showed that ASTM trace processing engages hierarchical cortical areas and clarified their interactions. Bottom-up signals flow from the insula and auditory temporal regions to the frontal lobe early on, followed by top-down information from the frontal lobe to the hippocampus, inferior temporal lobe, and insula at a later pre-attentive stage. Critically, Bayesian model selection of dynamic causal modeling revealed that deviant stimuli selectively enhanced the effectiveness of top-down connections to the hippocampus, thereby facilitating ASTM trace formation. These results provide compelling evidence that the human hippocampus contributes to auditory short-term memory at a pre-attention stage and suggests a challenge to entrenched beliefs in the classification of memory systems.

neuroscience↗

bioRxiv2025

A linear regression model predicts human brain ageing and reveals differential neuronal biological ageing relevant for Parkinson's disease susceptibility

Biological brain ageing is a major risk factor for neurodegenerative diseases, which are characterized by selective degeneration of particular neuron types. We analyzed the impact of ageing on the transcriptome of neurons in the ventral tegmental area (VTA), substantia nigra pars compacta (SNc) and locus coeruleus (LC), that show differential vulnerabilities to Parkinsons disease. Neurons were isolated from human post mortem brain tissues originating from 48 individuals ranging from 17 to 102 years of age and subjected to Smart-seq2 RNA sequencing. We identified 2,764 genes that were correlated with chronological ageing. This gene expression data was used to develop a feature selection-based Time Traversal algorithm, utilizing functionally grouped gene sets, GO terms, with high predictive accuracy of biological brain ageing. We identified 59 GO terms that can predict biological age using a linear regression model, where leave-one-out cross validation demonstrated a strong correlation between chronological age and predicted biological age (Pearson correlation coefficient = 0.946; adjusted R{superscript 2} = 0.771). The algorithm was validated on five independent datasets with high predictive performance, demonstrating shared ageing features across the human brain. Nonetheless, our analysis also highlights brain region and neuron type specificity in particular ageing features. Resilient neurons showed a weaker association with age-related transcriptional changes, indicating that they age slower than their vulnerable counterparts, thus revealing targets that may be used to slow down ageing and prevent disease development.

neuroscience↗

bioRxiv2025

High throughput quantitative tracking of single parasite in Plasmodium falciparum

New systematic profiling of drug effects is in demand due to limitations in existing approaches to evaluate comprehensive drug effects and distinguish heterogeneity in mixed populations. One challenge is the underdeveloped methods for investigation of causal association between artemisinin induced dormancy and recrudescence in Plasmodium falciparum. We developed Quantitative Tracking After Chemotherapy Exposure (qTRACE) and an artificial intelligence (AI) mode to evaluate cytotoxic and cytostatic effects simultaneously at single parasite resolution in a high throughput platform. qTRACE is based upon the observation that individual parasites grow into colonies that can be quantified for numbers of viability and growth rate. Applying qTRACE, we revealed parasite-drug killing dynamics after artemisinin exposure, finding up to 50% of viable parasites arise directly from recovery of artemisinin induced dormancy. We further developed next generation qTRACE integrated with deep learning-based segmentation and analysis, thereby directly linking continuous, time-lapse phenotypes of label-free live P. falciparum. Our results confirmed the viability of dormant ring stages and that recovery rates differ between artemisinin-susceptible and -resistant P. falciparum.

cell biology↗

bioRxiv2025

Antibody-Protein L Functionalized Microparticles for Detection of Surface Markers in Heterogeneous Colorectal Lesions

Visualization of colorectal cancer (CRC) lesions is complicated by their location in the colon and tumor morphology. Reliance on a single surface biomarker for direct identification risks false negatives due to temporal changes and/or tumor heterogeneity. We developed a multiplexed system of complementary biomarker targets in an effort to capture a broader range of lesions with diverse temporal and/or phenotypic expression. We identified Mucin-1 (MUC1) and epithelial cell adhesion molecule (EPCAM) as useful targeting pairs by examining multiple colon tumor subtypes in a standard tissue array, and by surveying multiple CRC cell lines, both as 2D cultures and as 3D tumoroids, for the presence of the CRC surface biomarkers. We demonstrated the utility of a "universal" surface functionalization approach using Antibody-Protein L functionalized microparticles (APL-MPs) that enabled the simultaneous incorporation of antibodies recognizing MUC1 and EPCAM. Using CRC cell heterogeneous tumoroids expressing both MUC1 and EPCAM (HET-tumoroids) and orthotopic animal cancer models designed to express both surface antigens, we demonstrated that: 1) APL-MPs identified MUC1- and EPCAM-positive tumoroids in proportion to antigen expression; 2) APL-MPs detected CRC surface antigens on the luminal colon surface in vivo, and 3) concurrent targeting of multiple surface antigens enhanced the sensitivity of detection of heterogeneous CRC lesions. This approach opens the door for the use of antibody-protein L dual-targeting MPs in a variety of applications to detect heterogeneous cancer lesions. SignificanceMulti-antigen targeting of MUC1 and EPCAM with Antibody-Protein L microparticles enhances the detection sensitivity of heterogeneous colorectal cancer lesions, offering a promising strategy for the accurate visualization of tumors in complex environments.

cancer biology↗

bioRxiv2025

ABA-responsive transcription factor CbNAC63 is involved in modulating biosynthesis of triterpenoid saponins in Conyza blinii

Conyza blinii, a traditional Chinese medicinal herb, accumulates triterpenoid saponins. NAC transcription factors (TFs) are pivotal for plant stress responses and hormone-mediated secondary metabolism, while abscisic acid (ABA) regulates terpenoid biosynthesis in medicinal plants. However, how NAC TFs mediate ABA-regulated triterpenoid saponin synthesis in C. blinii remains unclear. In order to address this gap, the focus was directed towards CbNAC63--a NAC TF identified from the nocturnal low-temperature transcriptome of C. blinii. Phylogenetic and motif analyses showed it belongs to the stress-responsive NAC subclade with conserved domains. Y2H assays revealed its self-interaction, enhancing transcriptional activity; subcellular localization confirmed nuclear localization. RT-qPCR results indicated CbNAC63 exhibits tissue-specific expression under nocturnal low-temperature stress, accompanied by increased triterpenoid saponin accumulation. ABA signaling primarily regulates this process: exogenous ABA enhanced CbNAC63 expression and saponin content, while fluridone suppressed both. Overexpression (OE) and virus-induced gene silencing (VIGS) demonstrated CbNAC63 positively regulates saponin biosynthesis. Y1H and dual-luciferase reporter assays confirmed CbNAC63 directly binds to the promoters of Cb{beta}AS and CbHMGR and activates their transcription. In summary, the study shows CbNAC63 integrates ABA and low-temperature signals, activating MVA pathway genes to regulate saponin synthesis. This unveils a novel "ABA-CbNAC63-MVA" module, enriches the classic regulatory network, and provides a target for improving medicinal plant quality. HighlightsIdentifies CbNAC63 as a novel regulator that integrates ABA and cold signals to boost saponin production in medicinal plants.

plant biology↗

bioRxiv2025

Ventral Hippocampal Temporoammonic and Schaffer Collateral Pathways Differentially Control Fear- and Anxiety-Related Behaviors

The ventral hippocampus plays a crucial role in regulating anxiety- and fear-related behaviors. Previously, we demonstrated that diazepam reduces anxiety-like behavior by inhibiting the dentate gyrus and CA3 principal neurons via 2-GABAARs, while inhibition of CA1 pyramidal neurons is necessary to suppress fear-related responses. This study investigated the role of inputs from ventral CA3 (vCA3) and entorhinal cortex to ventral CA1 (vCA1) in anxiety- and fear-like behavior using bidirectional optogenetic modulations. Adult C57BL/6J male and female mice were subjected to bilateral stereotaxic injection of a viral vector expressing channelrhodopsin or halorhodopsin into vCA3 or into layers II-III of lateral entorhinal cortex, followed by bilateral implantation of fiberoptic ferrules into vCA1. After four weeks of recovery, mice were assessed for anxiety-like behavior in the novel open field, elevated plus maze, and Vogel conflict tests, and by contextual and trace fear conditioning for fear. The behavior of the mice was recorded under laser ON and OFF conditions in all experiments. The activation of vCA3 to vCA1 projections (i.e., Schaffer collateral pathway) increased anxiety- and fear-related behaviors, whereas inhibition reduced such behaviors. In contrast, optogenetic activation or inhibition of EC to vCA1 projections (i.e., temporoammonic pathway) had no effect on anxiety-related behavior but positively or negatively modulated fear-related behavior, respectively. These results suggest that while fear-related behavior is modulated by both inputs to vCA1, modulation of anxiety-related behavior is input-specific for the vCA3 to vCA1 projection. In summary, this study offers mechanistic insights into the complex organization of hippocampal circuitry underlying fear and anxiety. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=183 SRC="FIGDIR/small/690696v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1a3a0d7org.highwire.dtl.DTLVardef@194b96forg.highwire.dtl.DTLVardef@11a62b7org.highwire.dtl.DTLVardef@1471977_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Charting the Undiscovered Metabolome with Synthetic Multiplexing

Most molecular features detected in untargeted metabolomics remain uncharacterized due to the limited scope of existing spectral reference libraries. We synthesized >100,000 biologically inspired compounds using multiplexed reactions, of which 91% were absent from existing structural databases, and searched the resulting MS/MS library across >1.7 billion public spectra, increasing annotation rates by 17.4%. This approach revealed previously undescribed exposure-derived metabolites, including ibuprofen-carnitine. Because ibuprofen has been linked to rhabdomyolysis, reduced mitochondrial function, and impaired muscle recovery in carnitine-limited contexts, we investigated the functional relevance of this conjugate. Ibuprofen-carnitine reduced carnitine transport via the OCTN2 transporter, and in a postpartum mouse muscle injury model, ibuprofen delayed muscle repair that could be rescued by carnitine supplementation, with urinary ibuprofen-carnitine:carnitine ratios tracking this effect. These findings support a hypothesis whereby NSAID-carnitine conjugates compete for carnitine transport, impairing energy metabolism and muscle recovery in susceptible individuals. Synthetic multiplexing thus provides a scalable route to annotate the dark metabolome and generate experimentally testable biological hypotheses.

biochemistry↗

bioRxiv2025

The 9p21.3 Coronary Artery Disease Risk Locus Modulates Vascular Cell-State Transitions via Enhancer-Driven Regulation of MTAP

The 9p21.3 locus is the strongest genetic association with coronary artery disease (CAD), yet its causal mechanisms remain unresolved. We map the regulatory architecture of 9p21.3 in disease-relevant vascular cells, identifying 12 enhancers within the CAD risk haplotype that respond dynamically to inflammatory and metabolic stress in fibroblasts and smooth muscle cells. These activated states are enriched for CAD heritability, implicating stress-responsive vascular wall cells in disease pathophysiology. Dense CRISPRi tiling integrated with fine-mapping and genomic constraint across >500,000 individuals nominates MTAP as the effector gene, with rs1537371 as a likely causal variant. Perturbation and multi-modal analyses show that MTAP loss induces pro-fibrotic and angiogenic programs and sensitizes vascular cells to TGF-{beta}-driven pathological transitions. Our findings reveal a vascular-specific enhancer network through which noncoding variation at 9p21.3 modulates CAD risk via MTAP--a previously unrecognized regulator of vascular remodeling located 269 kb from the risk haplotype. HighlightsO_LI9p21.3 CAD risk locus harbors 12 functional enhancers active in vascular wall cell types C_LIO_LICAD heritability is enriched in stressed vascular fibroblasts and smooth muscle cells C_LIO_LIHigh-resolution CRISPRi-MAC-seq maps 9p21.3 enhancer-gene and SNP-gene interactions C_LIO_LIMTAP identified as a causal effector gene regulated by 9p21.3 fine-mapped and constrained variants C_LIO_LIMTAP modulates TGF-{beta}-driven pathological vascular cell transitions C_LI

genomics↗