Nutrient profiling systems (NPS) are used to rank foods by nutrient composition to support public health policy and consumer guidance. Most existing NPS are designed for packaged foods and evaluate nutrients per 100 g or 100 mL, which may not reflect dietary patterns in cultures where home-cooked meals predominate. In Japan, excessive sodium intake, primarily from seasonings and condiments, remains a major public health issue. The Ajinomoto Group Nutrient Profiling System (ANPS) was developed to evaluate Japanese dishes and meals "as consumed," using culturally relevant serving sizes and four criteria: protein, vegetables, saturated fatty acids, and sodium. ANPS was validated using nutrient composition data from 1,089 dishes and 1,816 meals, including recommended, randomly generated, restaurant, and bento-box meals. Validation analyses examined correlations with established nutrient profiling and diet-quality indices. The ANPS showed moderate positive correlations with the Nutrient Rich Food Index (NRF6.3 for dishes, NRF9.3 for meals) and with meal-quality indicators, including the metric Healthy Eating Index 2015 (mHEI-2015). The system has been implemented in the multi-industry Tsujitsuma Shiawase project, where ANPS-based marks help guide consumers toward healthier choices through recipes and public campaigns. The ANPS offers a culturally appropriate and scientifically robust framework for evaluating Japanese meals and supporting sodium reduction. Limitations include exclusion of desserts and beverages in dishes and the lack of direct assessment of excess energy or sugar intake. Ongoing refinement and broader validation are needed to strengthen its usefulness for dietary assessment and public health promotion.
Excessive sodium intake remains a major public health issue in Japan, contributing to the burden of non-communicable diseases, such as hypertension. To address this, these authors developed two nutrient profiling models, one for processed foods and another for dishes, to guide food reformulation and promote healthier eating. This article focuses on the dish model, which can be applied to other regions where ready-to-eat meals are highly available. The Nutrient Profile Model for Dishes in Japan (NPM-DJ) was developed using data from the Japanese Food Guide Spinning Top and Japan's National Health and Nutrition Survey. Dishes were categorised to align with the traditional food culture and scored based on nutrient content per serving, including both nutrients to limit and nutrients to encourage. The NPM-DJ evaluates dishes holistically per serving, accounting for seasonings and oils. A scoring system subtracts positive nutrient points (fruits, vegetables, nuts/seeds, legumes, mushrooms, seaweed, protein, dietary fibre) from baseline points (energy, saturated fat, sugars, sodium). Example calculations demonstrate its utility in ranking the typical 105 Japanese dishes as shown in the Japanese Food Guide Spinning Top. The NPM-DJ offers a culturally relevant framework for improving dietary habits and guiding food reformulation. It supports public health initiatives and empowers consumers to make informed choices.
The present study reports the green synthesis of iron oxide nanoparticles (Fe3O4 NPs) using the ethanolic leaf extract of Rubus ellipticus (RE), supported by GC-MS profiling. 48 phytochemicals including stigmast-5-en-3-ol, phytol, linoleic acid ethyl ester, neophytadiene, and vitamin E acted as natural reducing and stabilizing agents. The RE-mediated Fe3O4 nanoparticles (RE-Fe) were characterized by using XRD, TEM-EDX, and the XPS analysis. XRD confirmed the highly crystalline, phase-pure magnetite with a cubic spinel structure, and TEM revealed about the quasi-spherical particles averaging 37.73 ± 6.03 nm. XPS validated the mixed Fe²⁺/Fe³⁺ oxidation states typical of the Fe3O4. The Biological evaluation showed the excellent antioxidant activity of the RE-Fe compared to the extract, with an IC50 values of 27.93 and 39.06 µg/mL in DPPH and the phosphomolybdate assays. Antidiabetic assays demonstrated the strong α-amylase and the α-glucosidase inhibition (IC50 = 49.54 and 35.21 µg/mL), outperforming the plant extract. RE-Fe also exhibited the potent antibacterial activity against the bacterial strains E. coli and S. aureus, comparable to ciprofloxacin. Molecular docking supported these outcomes, revealing strong interactions of key phytochemicals with TyrRS, DNA gyrase, α-amylase, and α-glucosidase. Overall, Rubus ellipticus is shown to be an effective source for eco-friendly Fe3O4 NPs synthesis with promising biomedical applications.
The stated purpose of nutrient profiling (NP) models is to help implement dietary guidelines by addressing prevailing health issues. In high-income countries, obesity and non-communicable diseases are the main health issues of concern. As a result, NP models typically penalize packaged processed foods that contain calories, total or added sugar, sodium, and saturated fat. This negative nutrition approach may not be optimal for Southeast Asia, where nutrient shortfalls and nutrient deficiencies are still prevalent. A more positive approach featuring nutrients to encourage might be more appropriate. NP models should incorporate protein, fibre, calcium, iron, zinc, vitamin A, B vitamins, vitamin B12, and vitamin E. The specific choice of index nutrients may depend on population health needs. Further, given the diversity of Asian food cultures, it may be time to go beyond packaged foods and apply the NP methodology to mixed dishes and to complete meals. This article illustrates the application of NP models to composite meals.
In Thailand, meals are commonly consumed as combinations of multiple dishes, yet no established nutritional criteria exist to evaluate the healthfulness of meals. This study aimed to develop healthy meal criteria for Thai diets using a nutrient profile model. The Nutrient Profiling System for Meals (NPS-M) was developed with six nutritional components: energy, protein, vegetables, total fat, added sugar, and sodium. A scoring algorithm was created. Meal combinations were considered healthier if they achieved scores ≥70%, with no zero score in any one component. A total of 72,149 meals were constructed and evaluated. Criterion validity was assessed by comparing NPS-M with the Nutrient-Rich Foods Index 6.3 (NRF6.3), Health Star Rating (HSR), and Thailand's Healthier Choice logo for ready-to-eat foods (HCL-RTE) using Spearman's rank correlation. The median NPS-M score of all meal combinations was 58 (interquartile range: 45.0-72.0). After excluding meals with zero scores in any component, 10,148 meals (14.1% of total) remained. Among these, 7,252 meals (10.1% of total) achieved scores ≥70%. Sodium was a predominant limiting factor, disqualifying 80% of meals. Criterion validity test-ing showed moderate correlation with NRF6.3 (ρ = 0.566, p <0.001), moderate reverse correlation with HSR (ρ = -0.527, p <0.001), and strong correlation with HCL-RTE (ρ = 0.796, p <0.001). The NPS-M provides a practical framework for evaluating meal healthfulness in the Thai context. The model has potential for use in restaurants, canteens, and public health programs to improve meal quality and support healthier diets in Thailand.
Insulin resistance (IR) correlates with a wide spectrum of diseases and death. However, the specific proteomic signatures of IR and their associations with health outcomes remain incompletely understood. Leveraging data of 2,920 plasma proteins from 19,556 individuals in UK biobank study, we employed the elastic net model to dissect IR-related proteins and construct proteomic signature scores. Cox proportional hazards model was fitted to examine the longitudinal associations of distinct IR indicators and their proteomic signatures with multiple chronic disease and mortality. Mediation analyses were conducted to explore the role of individual proteins and proteomic signatures in IR-disease associations. Over a mean follow-up of over 12 years, higher levels of IR surrogate makers were linked to cardiovascular-kidney-metabolic events and mortality, with eGDR outperforming other metrics in predictive discrimination. Furthermore, most IR proteomic signatures were prospectively associated with the incidence of type 2 diabetes mellitus, ischemic heart diseases, stroke, chronic kidney diseases, and mortality. Proteins associated with IR were primarily enriched in inflammation, immune response, and lipid metabolism, with immune-related proteins holding crucial roles. Multiple IR-disease associations were significantly mediated by proteomic signatures and specific proteins, like HAVCR1, CXCL17, and GDF15. This study probed into the plasma proteomic profiles in IR settings and the associations of relevant protein signatures with multiple chronic diseases and mortality, providing additional guidelines on targeted intervention strategies for cardiovascular-kidney-metabolic outcomes.
It is imperative to recognise that the main components of the food environment in SEA are not processed foods and the so-called ultra-processed foods. Instead, large segments of the population have their meals frequently away from home, as demonstrated by data from Malaysia and Indonesia in this supplement. A myriad of eating places have mushroomed in countries in the region, ranging from street foods, coffee shops, hawker centres and restaurants as well as through numerous food delivery services. Many of these meals are imbalanced, lacking in the healthful food groups, whilst containing high amounts of sugar, oil and salt. Frequent and excessive consumption of these meals and beverages could very well be the main contributors to the nutrition related health problems in the region. Recognising this, the supplement summarises research car-ried out on developing nutrient profiles based on meals or dishes as one of the strategies to improve the food environment. One article in this supplement summarises the principles and utilisation of nutrient profiles while another three articles summarise such meal-based profiles developed by researchers in Thailand and Japan. Meal-based nutritional profile systems, based on food cultures of countries in the region, could help both food vendors to reformulate and improve their menus as well as to consumers to select healthier away-from-home meals. It is hoped that information in this supplement may prove useful for researchers, policy makers, and health care professionals in their efforts to improve the food environment in SEA.
Numerous reports of drug resistance in Leishmania major, the causative agent of cutaneous leishmaniasis (CL), underscore the need to discover novel therapeutics. Fungal secondary metabolites (SMs) are valuable resources for drug development and can serve as antimicrobial agents, enzyme inhibitors, and lead compounds for novel medicines. A three-dimensional model of the L. major sterol 14α-demethylase (LmCYP51) enzyme was built using L. infantum CYP51 as a template. A library of 1,167 compounds was virtually screened against LmCYP51 using high-throughput docking. Eleven promising candidates were identified and further analyzed through 100-ns molecular dynamics simulations. Six high-affinity candidates were selected for experimental validation. In vitro assays, including MTT, Giemsa staining, and flow cytometry, were performed to evaluate antiparasitic efficacy. Dihydrocitrinone emerged as the most promising compound with the most negative predicted binding free energy (ΔG = -35.41 kcal/mol) and the most potent in vitro activity, with IC50 values of 9.87 and 26.29 µM against promastigotes and intracellular amastigotes, respectively. The compound exhibited moderate selectivity (selectivity index = 2.8). Flow cytometric analysis revealed that dihydrocitrinone, at its IC50 concentration, promotes phosphatidylserine externalization and induces apoptosis-like programmed cell death in 86% of cells. By integrating computational prioritization with experimental validation, this study identified dihydrocitrinone, a fungal polyketide, as an early antileishmanial hit against L. major that induces apoptotic-like programmed cell death. Dihydrocitrinone's promising antileishmanial potency provides a suitable scaffold for medicinal chemistry optimization and the development of novel therapeutics for leishmaniasis. This research provides the first experimental validation of dihydrocitrinone against L. major and highlights the underexplored potential of fungal SMs in antileishmanial drug discovery.
Amomi Fructus (Amomum villosum Lour.)-processed Rehmanniae Radix (Rehmannia glutinosa Libosch.) is a traditional Chinese herbal preparation used to tonify blood and improve digestive tolerance. It is considered a rational processing method to enhance the efficacy of Rehmanniae Radix (RR) in blood deficiency syndrome (BDS). This study investigated the therapeutic effects of Amomi Fructus -processed Rehmanniae Radix (AR) on BDS and explored its underlying mechanisms using a multi-omics approach. A rat model of BDS was established using cyclophosphamide and acetylphenylhydrazine. Rats were treated with AR or RR. Hematological parameters, spleen histopathology, TUNEL staining, bone marrow apoptosis by flow cytometry, transcriptomics, spleen metabolomics, and gut microbiota profiling were performed. AR significantly improved RBC, WBC, HGB, and HCT levels and alleviated spleen pathological injury in BDS rats. Transcriptomic analysis showed that the PI3K/Akt, and MAPK signaling pathway was significantly enriched among differentially expressed genes. AR reduced phosphorylation of PI3K, Akt, ERK, JNK, and p38, and markedly suppressed apoptosis in the spleen and bone marrow. Metabolomic profiling indicated that AR restored BDS-induced metabolic disturbances, while gut microbiota analysis showed that AR modulated microbial composition. Overall, AR produced more pronounced effects than RR. AR alleviated BDS in rats, potentially by inhibiting PI3K/Akt/MAPK-mediated apoptosis and restoring metabolic and microbial homeostasis. These findings support the traditional use of AR as a blood-tonifying herbal preparation.
The emergence of Androgen Receptor variants (AR-Vs) during hormonal treatment is believed to be one of the key mechanisms of resistance. AR-Vs lack the ligand-binding domain and function as constitutively active transcription factors, rendering AR-targeted endocrine-based therapeutics ineffective in tumors that express AR-Vs. The goal of this study was to develop a targeted multiplex assay to identify known and unexplored AR-V proteins and help guide the stratification of PCa patients based on their AR-V protein profiles. A targeted multiple reaction monitoring (MRM) assay using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed to quantify total AR proteins using the AR N-terminal domain (AR-Nterm), a well-characterized AR splice variant AR-V7 (AR-V7), a putative, previously identified but uncharacterized protein isoform (AR-V12) and isoforms that code for an exon 3 duplicated junction seen in AR-V2 and AR- full length with two copies of exon 3. Specimens included three AR-positive PCa cell lines (22Rv1, VCaP16, LNCaP), two AR-negative PCa cell lines (PC3, DU145), and a patient-derived xenograft (PDX) model of CRPC. Endogenous target peptides were quantified according to tier-2 targeted mass spectrometry "fit-for-purpose" guidelines to ensure analytical rigor. Analytical performance was characterized across a linearity range of 4.15 fmol to 4000 fmol followed by evaluations of precision, accuracy, selectivity, stability, ion suppression and repeatability studies. The overall coefficient of variation (CV) was < 20% across seven independent validation experiments. Endogenous AR-V peptides were accurately quantified using calibration curves, achieving acceptable linear regression coefficients (R2 > 0.95). Four targets, including AR-Nterm and 3 AR-variants, were identified and quantified in PCa cell lines and in a PDX pre-clinical model. This study establishes a robust, validated MRM targeted proteomics assay capable of reproducibly detecting and quantifying both known and previously uncharacterized AR-Vs at the protein level  . The assay demonstrated < 20% analytical variation at the lower limit of quantification of 4.25 femtomole (fmol) for AR-Nterm and 8.25 fmol for AR-V7, AR Exon3-Dup/AR-V2 and AR-V12 and, showed robust analytical performance in preclinical models and is ready for further evaluation in clinical specimens. This provides a clinically applicable platform for the comprehensive profiling of AR-V proteins in human subjects, enabling improved stratification of patients with CRPC and supporting precision therapeutic strategies.
Away-from-home meals have become an increasingly common part of the Malaysian diet, with the wide availability of hawker stalls, coffee shops, cafes, restaurants, and food delivery services catering to diverse tastes and budgets. This paper provides a narrative overview of the Malaysian context, based on relevant literature and policy initiatives. The growing eating-out practice is driven by urbanisation, lifestyle changes, limited time for home cooking, growing preference for convenience, and rising incomes. While eating out has become a social norm, its increased frequency raises nutrition and public health concerns. Local evidence shows that many commonly consumed hawker foods are high in sodium, sugar, and fat, while lacking healthful ingredients such as vegetables, potentially worsening Malaysia's already high burden of diet-related non-communicable diseases. Existing national policies and programmes, such as the Healthier Dining Programme, MyMeal, Healthy Cafeteria and Healthy Catering Trainings, provide nutrition and food safety criteria for healthier meal provision. However, their reach among informal food vendors remains limited, and data on consumer awareness and uptake are scarce. Strengthening and expanding these programmes to better include informal vendors is crucial to increasing the availability of healthier meals. Other opportunities include developing healthier reference recipes for commonly consumed hawker foods to guide reformulation, exploring meal-based nutrient profiling to inform meal selection, using digital nudges within food delivery platforms, and enhancing consumer education. There is also an urgent need for representative national data on away-from-home meals, including consumption patterns, perceptions, demand for healthier options, purchasing behaviours, and their contribution to overall diet and nutritional status.
Quinclorac is widely used in rice cultivation; however, its persistent residue poses a serious risk to subsequent tobacco crops in rice-tobacco rotation systems, limiting the sustainability of this practice. Although rice and tobacco exhibit markedly different sensitivities to quinclorac, the molecular basis for this divergence remains unclear. In this study, we investigated the differential molecular mechanisms from stress perception to phenotypic response by integrating comparative transcriptomics, physiological profiling, and metabolic pathway analysis. Under quinclorac, the tobacco cultivar K326 (K326) suffered severe growth inhibition and oxidative damage, whereas the rice cultivar Nipponbare (NPB) maintained internal homeostasis. Comparative transcriptomics analysis revealed putative distinct response strategies. K326 may activate a defense response program characterized by strong induction of mitogen-activated protein kinase (MAPK) and ethylene/jasmonic acid signaling pathways, followed by large-scale transcriptional reprogramming dominated by MYB and WRKY transcription factors. In contrast, NPB may adopt a steady-state prioritization strategy, upregulating NAC transcription factors to enhance glutathione-based detoxification while sustaining the core metabolic processes, including photosynthesis. Collectively, our work provides a systematic framework for understanding the molecular basis of the differential quinclorac response in rice and tobacco.
This study developed coaxially electrospun polycaprolactone/polyvinyl alcohol (PCL/PVA) core-shell nanofibrous scaffolds incorporating green-synthesized silver nanoparticles (AgNPs) from Synedrella nodiflora as candidate antibacterial wound-dressing materials. The core-shell design was evaluated against a conventional blended PCL/PVA/AgNP control at the same AgNP loading to assess architecture-dependent performance. Transmission Electron Microscopy (TEM) analysis supported the formation of a distinguishable PCL/PVA core-shell structure, while Scanning Electron Microscopy (SEM) showed uniform, bead-free fibers, with diameter reduced from 332 nm to 310 nm after AgNP incorporation. Fourier Transform Infrared Spectroscopy (FTIR) analysis supported the presence of hydroxyl-containing phytochemical residues or polar functional groups associated with the green-synthesized AgNPs. Moisture management properties improved, with Overall Moisture Management Capacity (OMMC) increasing from 0.16 to 0.74 and Accumulative One-Way Transport Index (AOTI) shifting from -28.6 to 310.2, indicating improved liquid transport under MMT conditions. Thermal stability also increased, with degradation temperature rising from 378 °C to 392 °C and residual weight from 5.2% to 6.3%. Mechanical strength decreased slightly with AgNP addition, while elongation remained relatively high, showing a trade-off between strength and flexibility. UV-Vis-based apparent silver-associated release profiling showed a slower release trend for coaxial PP-3% than blended Control-3%. PP-3% exhibited the highest preliminary antibacterial activity, with inhibition zones of 22 mm against E. coli and 17 mm against S. aureus. Vero cell viability remained above 90%, indicating preliminary cytocompatibility.
Deep reinforcement learning (DRL) remains constrained by high computational costs, hindering its practical deployment. While neural network pruning offers a solution for model compression, most existing DRL approaches rely on unstructured pruning. This results in irregular sparse matrices that lack compatibility with standard hardware, offering no tangible real-time acceleration. Furthermore, pruning in DRL is notoriously challenging due to inherent training instability, which often leads to catastrophic performance degradation. To overcome these limitations, we propose a novel framework that integrates dynamic structured pruning with model merging. By periodically merging parallel network instances, our method effectively counteracts the instability triggered by aggressive structural changes, enabling the use of structured pruning directly compatible with general-purpose hardware. Experimental results on continuous control tasks demonstrate that our approach reduces cumulative training FLOPs by up to 72% while maintaining performance competitive with dense baselines across the majority of environments. Additionally, inference profiling confirms an average latency reduction of 16.2%, highlighting the framework's potential for accelerating both the training and deployment of DRL agents. Our code is available at https://github.com/hail-mary/neuron-pruning.
Pseudomonas aeruginosa is a clinically significant opportunistic pathogen characterized by intrinsic and acquired resistance mechanisms coupled with a diverse array of virulence determinants. This study investigated the distribution of P. aeruginosa in various clinical specimens (n = 382), its virulence genes, antimicrobial resistance patterns, and associations with total resistant P. aeruginosa (TRPA) phenotypes. The majority of isolates were recovered from sputum (24.3%) and endotracheal tube samples (22.5%). Virulence gene screening revealed moderate-to-high prevalence of lasB (55.0%), toxA (49.7%), pilA (53.7%), aprA (56.5%), phzS (45.0%), exoS (41.9%), and exoU (38.0%), indicating their widespread involvement in pathogenicity. Antimicrobial susceptibility profiling demonstrated the highest susceptibility to amikacin (56.3%) and gentamicin (52.4%), while resistance to carbapenems (imipenem 52.4%, meropenem 52.9%) and cephalosporins was alarmingly high. Based on resistance classification, 33.5% of isolates were MDR, and 9.7% XDR. Among ceftazidime-resistant isolates (n = 200), 83% harboured ESBL genes, with blaCTX-M (38.0%) being most prevalent. Notably, 30.7% and 22.8% of isolates carried blaNDM-1 and blaOXA-48, respectively. Comparative analysis demonstrated statistically significant associations between TRPA phenotype and virulence genes: lasB (OR = 90.3), toxA (OR = 260.9), and pilA (OR = 32.6) (p < 0.0001). Resistance determinants such as blaCTX-M (OR = 3.5), aac(6')-Ib (OR = 2.9), qnrA (OR = 3.9), and co-carriage of NDM-1 + OXA-48 (OR = 4.9) were significantly enriched in TRPA isolates. These findings demonstrate a significant association between virulence and antimicrobial resistance traits, emphasizing the potential expansion of high-risk P. aeruginosa clones in clinical settings and highlighting the need for genomic surveillance and antimicrobial stewardship interventions.
Chicken skin colour is an economically important trait influenced by consumer preferences across different markets. Previous studies established that white skin is dominant over yellow skin, with the β, β-carotene-9',10'-dioxygenase (BCO2) identified as the candidate gene. However, the precise causal mutation within this gene region has remained unidentified for over a decade, limiting the development of reliable molecular markers for breeding programs. Through genome-wide association analysis of 381 chickens, we confirmed that the BCO2 gene region on chromosome 24 was the major locus associated with skin colour. Transcriptome analysis revealed approximately 590-fold higher BCO2 expression in white-skinned than yellow-skinned chickens. By integrating whole-genome sequencing data from 63 individuals with high-quality genome assemblies, we identified a 24-bp insertion that showed near-complete co-segregation with the yellow skin phenotype in a backcross family of 180 individuals. Electrophoretic mobility shift assays revealed an insertion-dependent DNA-protein interaction, and DNA pull-down coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) prioritised lymphoid enhancer-binding factor 1 (LEF1) as a leading candidate interactor. Chromatin profiling revealed elevated trimethylation of histone H3 at lysine 27 (H3K27me3) and reduced chromatin accessibility at the gene locus in yellow-skinned chickens. Functional experiments revealed that knockdown of LEF1 or inhibition of enhancer of zeste homologue 2 (EZH2) significantly increased BCO2 expression, supporting a model in which the insertion is associated with LEF1/EZH2-sensitive, polycomb repressive complex 2 (PRC2)-linked repression and transcriptional silencing. The 24-bp insertion in the BCO2 regulatory region is a candidate causal variant for yellow skin in chickens, refining the genetic model of chicken skin colour variation and supporting a LEF1-PRC2-associated regulatory mechanism potentially involved in avian carotenoid metabolism. This finding enables the development of a reliable PCR-based diagnostic marker for skin colour, facilitating marker-assisted selection in poultry breeding and providing new insights into the genetic regulation of avian pigmentation.
Accurate identification of ultra-low-frequency tumor-derived variants is critical for circulating tumor DNA (ctDNA)-based minimal residual disease (MRD) profiling. However, current ctDNA analysis workflows largely operate as predefined, sequential pipelines without explicit mechanisms for continuous monitoring of variant-calling performance or adaptive control, thereby limiting detection stability in genomically heterogeneous regions. To address this limitation, we developed MRDsteer, an autonomous closed-loop agent driven by artificial intelligence (AI). MRDsteer monitors the analytical reliability of variant calling during the analysis process using multidimensional quality metrics, such as filtration ratio and strand bias. When the estimated reliability falls below an actionable threshold, MRDsteer triggers localized re-calling only in high-risk genomic regions, instead of repeating the entire analysis. In this way, MRDsteer provides closed-loop control by continuously assessing variant-calling reliability and applying targeted intervention when needed. Comparative analyses in simulated and real-world datasets showed that MRDsteer improved the stability and sensitivity of ctDNA variant detection. Under challenging conditions, including ultra-low variant allele frequencies, MRDsteer demonstrated improved detection performance compared with representative baseline methods. In clinical cohorts, MRDsteer improved ctDNA-based MRD stratification and strengthened progression-free survival separation in the K438 cohort, including both non-small cell lung cancer (NSCLC) and nasopharyngeal carcinoma (NPC) subgroups. These results suggest that MRDsteer may provide a robust and clinically useful computational strategy for sensitive MRD detection and longitudinal ctDNA monitoring. https://github.com/aAT0047/MRDsteer.git.
Despite substantial clinical benefit from immune checkpoint inhibitors (ICI), advanced melanoma remains challenging due to frequent treatment resistance. Resistance may be intrinsic (primary) or emerge over time (secondary). Biomarkers predicting distinct resistance phenotypes before therapy are lacking. As key mediators of cellular communication, extracellular vesicles (EVs) represent promising biomarkers. This study aimed to identify baseline EV proteome-derived pathways and biomarkers associated with overall, primary, and secondary resistance to ICI in advanced melanoma and to derive biomarker signatures predictive of progression-free survival (PFS). EVs were isolated from pretreatment plasma samples of 46 patients with advanced melanoma using size exclusion chromatography and ultracentrifugation. Proteomic profiling was performed by liquid chromatography-mass spectrometry using DIA-NN. Pathway enrichment and network analyses were conducted using Reactome, Metascape, Cytoscape, and DAVID. Resistance-associated proteins were integrated into composite biomarker signatures and evaluated for association with PFS. Overall resistance was characterized by enrichment of platelet- and complement-associated pathways. Primary resistance was associated with enhanced Fc gamma receptor (FCGR) signaling and downregulation of KSRP-associated post-transcriptional regulatory processes. In contrast, secondary resistance was preceded by distinct baseline EV proteomic patterns involving complement activation and reduced hemostasis- and platelet-related pathways. EV-derived biomarker signatures for overall, primary, and secondary resistance independently discriminated patients according to PFS. Baseline plasma EV proteomics reveals distinct systemic biological programs associated with different resistance phenotypes to ICI in advanced melanoma. EV-derived biomarker signatures enable stratification by PFS and warrant validation in larger, multicentric cohorts.
Patients with insulin resistance exhibit reduced cardiorespiratory fitness (CRF), assessed by peak oxygen consumption (VO₂peak), compared with healthy age-matched individuals. Although high-intensity interval training (HIIT) can substantially improve VO₂peak, there is considerable interindividual variability in this response. Therefore, further research is needed to elucidate the molecular mechanisms underlying the heterogeneous response of VO₂peak to HIIT in individuals with prediabetes. Proteomic analyses of serum samples, along with fecal metagenomic and targeted metabolomic profiling, were conducted in medication-naïve, overweight and obese Chinese men with prediabetes (n = 35; aged 24-62 years). All participants underwent a 12-week HIIT intervention, and biological samples were collected both before and after the intervention to evaluate exercise-induced alterations in circulating proteins, gut microbial composition, and metabolite profiles. After 12 weeks of HIIT, mean VO₂peak increased by 0.47 L/min with individual responses ranging from 0 to 1.7 L/min. Baseline levels of short-chain fatty acid (SCFA)-producing genera, including Prevotella (β = 105.65, P = < 0.001, FDR = 0.034), Coprococcus (β = 50.22, P = 0.01, FDR = 0.39), and Hungatella (β = 40.72, P = 0.025, FDR = 0.50), were positively associated with ΔVO₂ peak. In contrast, baseline levels of the erythropoiesis-stimulating hormone erythropoietin (EPO) (β = -279.03, P = 0.024, FDR = 0.99) were negatively associated with ΔVO₂ peak. Exercise-induced changes in growth hormone 1 (β = 63.97, P = 0.04, FDR = 0.99) were positively associated with ΔVO₂ peak, whereas exercise-induced changes in BTB and CNC Homology 1 (β = -250.82, P = 0.01, FDR = 0.99), a repressor of heme oxygenase-1, were negatively associated with ΔVO₂ peak. In multiple linear regression analysis including clinical variables, percentage lean mass (β = 64.17, P = 0.0005) was the strongest variable associated with ΔVO₂peak. The clinical model explained 27% of the variance which increased to 37% (P = 0.002) upon inclusion of exercise-associated circulating factors such as EPO. Our findings reveal that baseline proteomic and metagenomic signatures are associated with VO₂peak adaptations. These multi-omics signatures may support the clinical implementation of personalized exercise interventions to improve CRF in individuals with prediabetes.
Methicillin-resistant Staphylococcus aureus (MRSA) is a major multidrug-resistant human pathogen. Vancomycin has long been the cornerstone therapy for invasive MRSA infections. Although nearly all MRSA isolates are susceptible to vancomycin in standard antimicrobial susceptibility testing, vancomycin treatment failure in MRSA bloodstream infections approaches 30%, and the underlying mechanisms remain poorly defined. Here, we show that subinhibitory concentrations of vancomycin promote MRSA survival within macrophages by hijacking host macroautophagy/autophagy. Using in vitro and in vivo models, we demonstrate that vancomycin exacerbates S. aureus-induced autophagic flux blockade, facilitating bacterial persistence. Mechanistically, this effect is not caused directly by vancomycin but by extracellular vesicles (EVs) secreted by S. aureus under conditions of vancomycin stress. These EVs exhibit a potent capacity to disrupt autophagosome-lysosome fusion, leading to the accumulation of autophagosomes. Proteomic profiling revealed a significant enrichment of the toxin α-hemolysin (Hla) in EVs derived from vancomycin-stressed bacteria. Deletion of the hla gene in S. aureus substantially attenuates the autophagy-disrupting capacity of vancomycin-induced EVs. Furthermore, recombinant α-hemolysin directly impaired autophagic flux in macrophages. RNA-sequencing and mechanistic analyses identified the PI3K-AKT pathway as a key signaling axis downstream of Hla, and this mechanism was further confirmed to mediate the autophagic degradation blockade induced by EVs from vancomycin-stressed S. aureus. Collectively, vancomycin triggers S. aureus to secrete EVs enriched with α-hemolysin, which potently inhibit autophagosome-lysosome fusion and promote intracellular MRSA survival. These findings provide critical insights into vancomycin treatment failure and identify bacterial EVs and α-hemolysin as potential therapeutic targets.