PubMed

Semin Arthritis Rheum. 2025 Feb 23:152696. doi: 10.1016/j.semarthrit.2025.152696. Online ahead of print.ABSTRACTTo enhance our understanding of the pathogenesis of diseases, including rheumatic diseases, and to improve disease control, it is essential to attain a thorough understanding of the human immune system, alongside mouse immunology. Historically, the investigation of the human immune system has posed significant challenges due to methodological limitations. Nonetheless, recent advancements in genomic studies of multifactorial diseases have elucidated that numerous risk-associated genetic variants affecting quantitative differences in cell-specific gene expression. In light of these findings, we are currently examining individual genetic variations in both healthy individuals and patients, as well as categorizing cells into distinct subsets in order to construct a comprehensive dataset concerning the human immune system. This is accomplished by combining data on gene expression, factors influencing the expression mechanisms, protein expression, metabolomics, and environmental variables pertinent to immune functionality-such as gut microbiota. These datasets will facilitate the comprehensive characterization of the human immune system. Using these datasets and through the integrative analyses of data related to risk genetic variations and gene expression profiles of each disease and individual, we anticipate uncovering novel insights into the human immune system, the heterogeneity of diseases, immune function mechanisms, and their regulatory strategies that may not be achievable through murine models.PMID:40037996 | DOI:10.1016/j.semarthrit.2025.152696

Carbohydr Polym. 2025 May 1;355:123367. doi: 10.1016/j.carbpol.2025.123367. Epub 2025 Feb 10.ABSTRACTPectins have demonstrated significant prebiotic potential in modulating gut microbiota and enhancing microbial metabolic functions. Nevertheless, the exact relationship between pectin structure and related properties on gut microbiota regulation is yet to be fully elucidated. To explore this, the interactions between four purified pectins with specific structural characteristics and gut microbiota were examined and compared through in vitro fecal fermentation, followed by full-length 16S rRNA gene sequencing, metabolomics, and bioinformatic analysis. The result shows that the pectins selectively modulated the composition of gut microbiota while being degraded into different levels of SCFAs. Moreover, the metabolite profiles in the pectin groups were also qualitatively and quantitatively different, suggesting that the structural variations in pectins further impacted the metabolic functionality of gut microbiota. The bioinformatic analysis revealed that various structural parameters of pectins, including the α-(1 → 4)-linked galacturonic acid composed linear chain in smooth region, arabinose residue determined hair region contribution, conjugated protein content, and molecular weight, are crucial factors in controlling their interaction with gut microbiota, the bacterial cross-feeding, and finally the microbial metabolic outcomes. This research advances our current understanding of the connection between pectin structure and its regulatory properties on gut microbiota at the level of purified pectin molecules.PMID:40037737 | DOI:10.1016/j.carbpol.2025.123367

Carbohydr Polym. 2025 May 1;355:123311. doi: 10.1016/j.carbpol.2025.123311. Epub 2025 Jan 24.ABSTRACTDiabetic nephropathy is a significant microvascular complication of diabetes mellitus. Crude polysaccharides extracted from red kidney beans and small black soybeans (RK, SB) have demonstrated promising antidiabetic effects in type 2 diabetic rats. This study evaluated the protective effects of RK and SB on kidney function in diabetic rats by examining kidney markers and urine metabolism. It also investigated the impact of pure polysaccharides (RKP, SBP) to pinpoint the active component of RK and SB. Findings indicated that RK and SB influenced kidney function by affecting the kidney index and key urine metabolites, like citric acid and cis-aconitic acid, linked to the TCA cycle and phenylalanine metabolism. Furthermore, a higher dose (400 mg/kg) of RKP and SBP was more effective in treating kidney damage in diabetic models than the optimal 200 mg/kg dose of RK and SB. This was shown by better regulation of urea nitrogen and uric acid levels, improved kidney tissue health seen in HE staining, and fewer red-stained lipid droplets in the kidney, as indicated by Oil Red O staining. Overall, this study provided additional evidence to support RKP and SBP as a functional ingredients production in the food industry.PMID:40037720 | DOI:10.1016/j.carbpol.2025.123311

Brief Bioinform. 2025 Mar 4;26(2):bbaf080. doi: 10.1093/bib/bbaf080.ABSTRACTComprehensive 2D gas chromatography coupled with mass spectrometry (GC × GC-MS) is a powerful analytical technique. However, the complexity and volume of data generated pose significant challenges for data processing and interpretation, limiting a broader adoption. Chemometric approaches, particularly multiway models like Parallel Factor Analysis (PARAFAC), have proven effective in addressing these challenges by enabling the extraction of meaningful chemical information from multi-dimensional datasets. However, traditional PARAFAC is constrained by its assumption of data tri-linearity, which may not be valid in all cases, leading to potential inaccuracies. To overcome these limitations, we present GcDUO, an open-source software implemented in R, designed specifically for the processing and analysis of GC × GC-MS data. GcDUO integrates advanced chemometric methods, including both PARAFAC and PARAFAC2, for a more accurate and comprehensive analysis. PARAFAC is particularly useful for deconvoluting overlapping peaks and extracting pure chemical signals, while PARAFAC2 relaxes de tri-linearity constraint, allowing the alignment between samples. The software is structured into six modules-data import, region of interest (ROI) selection, deconvolution, peak annotation, data integration, and visualization-facilitating comprehensive and flexible data processing. GcDUO was validated against the gold-standard software for comprehensive GC, demonstrating a high correlation (R2 = 0.9) in peak area measurements, confirming its effectiveness and reliability. GcDUO provides a valuable, open-source platform for researchers in metabolomics and related fields, enabling more accessible and customizable GC × GC-MS data analysis.PMID:40037642 | DOI:10.1093/bib/bbaf080

J Econ Entomol. 2025 Mar 3:toaf044. doi: 10.1093/jee/toaf044. Online ahead of print.ABSTRACTThe tea aphid Toxoptera aurantii Boyer (Hemiptera: Aphididae) is a destructive pest that infests tea plants. The resistance mechanisms of the tea plant against T. aurantii infestation are largely unexplored. This study investigates the defensive response of tea plants to T. aurantii feeding using an aphid-resistant Camellia sinensis cultivar 'Qiancha1' (QC1) and an aphid-susceptible C. sinensis cultivar 'Huangjinya' (HJY). Transcriptomics and metabolomics analyses were conducted on 4 samples: QCCK (T. aurantii non-infested QC1), HJYCK (T. aurantii non-infested HJY), QC24 (T. aurantii-infested QC1 for 24 h), and HJY24 (T. aurantii-infested HJY for 24 h). The results showed that the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in the 2 comparison groups (QCCK vs. QC24 and HJYCK vs. HJY24) were primarily enriched in metabolic pathways, including hormone signal transduction, phenylpropanoid biosynthesis and flavonoid biosynthesis. Following aphid infestation, the resistant cultivar QC1 exhibited more DEGs and DAMs than the susceptible cultivar HJY, indicating a stronger response to T. aurantii feeding stress. Additionally, the expression of phenylpropanoid- and flavonoid-related genes (CYP, 4CL, FLS, F3H, and LAR) was significantly upregulated in the resistant cultivar QC1 compared with that in the susceptible cultivar HJY. Metabolites involved in phenylpropanoid/flavonoid pathways, such as p-coumaroyl-CoA, caffeoylquinic acid, and feruloyl-CoA, were exclusively induced in QC1. These findings suggest that phenylpropanoid/flavonoid pathways play pivotal roles in tea plant resistance to T. aurantii infestation, providing valuable insights for the breeding and utilization of resistant germplasms.PMID:40037569 | DOI:10.1093/jee/toaf044

Open Biol. 2025 Mar;15(3):240285. doi: 10.1098/rsob.240285. Epub 2025 Mar 5.ABSTRACTMetabolic processes in fetuses can significantly influence piglet weight at birth. Understanding the genetic determinants of systemic metabolism is crucial for uncovering how genetic and molecular pathways impact biological mechanisms, particularly during the fetal phase. We present data on 1112 plasma metabolites using untargeted ultra-high performance liquid chromatography-tandem mass spectrometry methods, of 260 backcross (BC) fetuses from two sires' breeds at 63 days post-conception. Eight chemical superclasses have been identified, with lipids accounting for the majority of metabolites. Genomic heritability (h²) was estimated for each metabolite, revealing that 50% had h² values below 0.2, with a higher average in the amino acid class compared with the lipid. We annotated 448 significant metabolite quantitative trait loci associated with 10 metabolites, primarily lipids, indicating strong genetic regulation. Additionally, metabolite associations with sex, fetal weight and sire's breed were explored, revealing significant associations for 354 metabolites. Fetal weight influenced the largest number of metabolites, particularly glycerophospholipids and sphingolipids, emphasizing the genetic and metabolic complexity underlying fetal development. These findings enhance our understanding of the genetic regulation of metabolite levels and their associations with key phenotypic traits in fetuses, providing insights into metabolic pathways, potential biomarkers and serving as a baseline dataset for metabolomics studies of fetuses.PMID:40037532 | DOI:10.1098/rsob.240285

J Clin Endocrinol Metab. 2025 Mar 3:dgaf131. doi: 10.1210/clinem/dgaf131. Online ahead of print.ABSTRACTCONTEXT: Tangier disease (TD) is a rare, autosomal recessive genetic disorder associated with a deficiency in cellular cholesterol export leading to cholesterol accumulation in peripheral tissues. With approximately 150 described cases, the disease is significantly understudied, and the clinical presentation appears to be heterogenous.OBJECTIVE: To investigate the phenotype and lipid metabolism in TD.DESIGN: Multicenter cohort study.PATIENTS: Four patients with TD.MAIN OUTCOME MEASURES: Nuclear magnetic resonance (NMR)-based lipidomic and metabolomic analyses were performed in patients with TD and healthy controls.RESULTS: While showing similar laboratory patterns with respect to high-density lipoprotein depletion, the clinical phenotypes of four TD patients were heterogenous with two patients diagnosed at 47 and 72 years having predominantly gastrointestinal and neurological phenotypes. Two previously undescribed variants (c.2418G>A, c.5055.del) were reported.Apart from pathognomonic changes in HDL composition, NMR spectroscopy revealed an increased abundance of VLDL with higher total lipid and cholesterol concentrations, pointing towards an impaired clearance of triglyceride-rich lipoproteins. Increased triglyceride-rich IDL supports impaired hepatic lipase activity, together with a CETP-mediated increase in LDL-triglycerides at higher abundance of large LDL subtypes and decreased small dense LDL.The lipid composition of HDL particles and LDL-1/LDL-4 remained the strongest differentiating factors as compared to healthy controls.CONCLUSIONS: Clinical phenotypes of TD can be heterogeneous including gastrointestinal and neurological manifestations. Impaired triglyceride-rich lipoprotein clearance and hepatic lipase activity could be a pathophysiological hallmark of TD.PMID:40037526 | DOI:10.1210/clinem/dgaf131

Fish Shellfish Immunol. 2025 Mar 2:110246. doi: 10.1016/j.fsi.2025.110246. Online ahead of print.ABSTRACTMytilus live in water as sessile filter feeders, and the mantle tissue plays an important role in their immune defense. However, the overall knowledge of the immunity of this tissue remains limited. Peptidoglycan (PGN) and lipopolysaccharide (LPS) are the most representative microbe-associated molecular patterns (MAMPs) that play roles in the immune stimulation of host cells. In the present study, ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS)-based metabolomic analysis was performed to understand the precise regulatory mechanism at the molecular level in the Mytilus mantle in response to PGN and LPS stress. Moreover, the antioxidant ability and free amino acid composition of the mantle, and the antimicrobial activities of mantle mucus were evaluated. Our results revealed that LPS and PGN stresses had different effects on the mantle's free amino acid composition and antioxidant ability, and the mantle mucus' antimicrobial activity. Both PGN and LPS stress-induced alterations in amino acids, phospholipids, fatty acids, nucleotides, and their derivatives in the mantle. PGN injection activated the amino acid-related metabolism, and inhibited the lipid-related metabolisms in the mantle, while LPS injection activated the amino acid-related metabolisms and inhibited the arachidonic acid metabolism in the mantle compared to that in the control group. In addition, activation of the mTOR and FoxO signaling pathways and inhibition of lipid-related metabolism were observed in PGN vs. LPS. In addition, PGN injection induced the upregulation of fosfomycin and deoxynojirimycin in the mantle compared to LPS injection. Our study highlights the different responses at the metabolomic level of the mussel mantle to different MAMPs and the potential application of metabolites that specifically respond to PGN and LPS challenges in mussels as biomarkers.PMID:40037495 | DOI:10.1016/j.fsi.2025.110246

Environ Pollut. 2025 Mar 2:125964. doi: 10.1016/j.envpol.2025.125964. Online ahead of print.ABSTRACTThe association of individual metals in PM2.5 with cardiovascular damage has been established in previous studies, but there are fewer studies on co-exposure to multiple metals and potential metabolic alterations in cardiovascular damage. To investigate the early cardiovascular effects of multiple metals and the mediating effects of metabolites, we conducted a panel study on young adults from 2017 Winter to 2018 Autumn in Caofeidian, China. A total of 180 serum samples were analyzed for metabolomic profiles using liquid chromatography-mass spectrometry. The associations between personal metal exposure, metabolite levels, and indicators of cardiovascular injury were analyzed by linear mixed-effects modeling (LEM) and Bayesian kernel machine regression (BKMR). Metabolomic analyses showed 79 metabolites in the serum of healthy adults changed significantly between seasons and all metabolites were strongly associated with toxic metals. Additionally, differential metabolites were enriched in seven metabolic pathways and activated by metal exposure, such as Butanoate metabolism and Linoleic acid metabolism. BKMR model interpreted that the overall effect of metals mixture was negatively associated with Capryloyl glycine and Sphinganine and Sb mainly contributed to the effect. The results of mediation analysis revealed that the association between V and VEGF was mediated by Diethylhexyl with a partial proportion of 13.4%. Furthermore, the result also found the association between CerP(d18:1/26:1(17Z)) and ET-1 was mediated by TGFβ1 with a proportion of 53.4%. Our findings suggested that multiple metal exposure was associated with metabolomic changes of cardiovascular damage in young adults, and may simultaneously affect the metabolomic changes by inducing oxidative stress and inflammation.PMID:40037427 | DOI:10.1016/j.envpol.2025.125964

Cell Metab. 2025 Feb 28:S1550-4131(25)00021-X. doi: 10.1016/j.cmet.2025.01.021. Online ahead of print.ABSTRACTBRAF V600E-inhibition effectively treats melanoma, but acquired resistance rapidly develops. Protein expression profiles, mitochondrial energetics, metabolomics and fluxomics data in cell line, xenograft, and patient-derived xenograft systems revealed that concerted reprogramming of metabolic pathways (including glutaminolysis, glycolysis, TCA cycle, electron transport chain [ETC], and transsulfuration), along with an immediate cytoprotective response to drug-induced oxidative stress, underpins drug-tolerant persister cancer cell survival. Realignment of cysteine (Cys) metabolism, in particular an immediate upregulation of cystathionine-γ-lyase (CSE), was vital in persister cells. The oxidative cellular environment, drug-induced elevated cystine uptake and oxidative Cys catabolism, increased intracellular cystine/Cys ratios, thereby favoring cystine as a CSE substrate. This produces persulfides and hydrogen sulfide to protect protein thiols and support elevated energy demand in persister cells. Combining BRAF V600E inhibitors with CSE inhibitors effectively diminished proliferative relapse in culture models and increased progression-free survival of xenografted mice. This, together with induced CSE expression in patient samples under BRAF-V600E-inhibition, reveals an approach to increase BRAF-V600E-targeted therapeutic efficacy.PMID:40037361 | DOI:10.1016/j.cmet.2025.01.021

Plant Physiol Biochem. 2025 Feb 26;222:109677. doi: 10.1016/j.plaphy.2025.109677. Online ahead of print.ABSTRACTThe genus Isodon is recognized as a primary source for the production of ent-kaurane-type diterpenes and previous studies predominantly focused on ent-kaurene and miltiradiene as the most extensively investigated diterpenes in Isodon. The diversity of diterpene synthases within this genus has recently been acknowledged, while such studies have been largely restricted to single species. In this study, we systematically mined and functionally validated diterpene synthases from three Isodon species using transcriptomic and metabolomic analyses. We identified the expression profiles of genes associated with diterpene biosynthesis and integrated these data with metabolomic results to elucidate their roles within the diterpene biosynthetic pathway. By reconstructing the metabolic pathways in Escherichia coli, we functionally characterized 11 diterpene synthases and elucidated the biosynthetic pathways of several diterpene skeletons originated from nor or ent-CPP, including the previously reported skeletons like ent-kaurene and miltiradiene, as well as four skeletons (ent-13-epi-sandaracopimaradiene, ent-neoabietadiene, abieta-8(14)-en-13-ol synthase and sandaracopimaradiene) whose biogenesis was reported in Isodon genus for the first time. This study provides novel insights into the molecular basis underlying diterpene diversity in Isodon and establishes a valuable resource for the development of new bioactive molecules and potential drug lead compounds.PMID:40037178 | DOI:10.1016/j.plaphy.2025.109677

Ecotoxicol Environ Saf. 2025 Mar 3;292:117967. doi: 10.1016/j.ecoenv.2025.117967. Online ahead of print.ABSTRACTExcessive intake of essential and toxic metals affects the pathological process of osteoporosis. At present, the effects of single forms of iron (Fe), lead (Pb) and other metals on bone injury have been widely studied. However, these metal elements usually do not exist in the environment in a separate form. They are ingested in various ways and are often found together in the human body. However, the mechanism of bone damage caused by Fe and Pb mixed exposure is still unclear at this stage. At present, the combined analysis of multi-omics is the conventional method to explore the molecular mechanism behind the disease. Therefore, we attempted to combine proteomics and metabolomics to explain the mechanism of bone damage caused by mixed Fe and Pb exposure. Differential proteins and metabolites were found to be predominantly enriched in the JAK-STAT signalling pathway, inflammatory bowel disease (IBD), and osteoclast differentiation. Combined analysis showed that Fpr2, Lifr, Lisofylline, 7-Ketocholesterol, LacCer (d18: 1/14:0) and other substances may be involved in the process of bone injury mediated by mixed metal exposure. In summary, we hypothesise that mixed exposure to Fe and Pb leads to osteoclast activation via the JAK-STAT signalling pathway in situ and indirectly via the gut-bone axis, resulting in bone damage. In general, our study potentially suggests that bone injury induced by mixed exposure of Fe and Pb may be related to osteoclast proliferation mediated by changes in inflammatory levels in vivo.PMID:40037083 | DOI:10.1016/j.ecoenv.2025.117967

Food Chem. 2025 Feb 26;477:143526. doi: 10.1016/j.foodchem.2025.143526. Online ahead of print.ABSTRACTThis study integrated non-targeted metabolomics with chemometric analyses to dissect the impact of varying shell ratios on the distribution of free (FP) and base-bound (BP) polyphenols from C. oleifera seeds during pressing. We quantified a comprehensive 209-parameter set, encompassing 177 individual polyphenols, via UPLC Q-TOF MS, and analyzed the data using multivariate statistical techniques. PCA model exposed intrinsic variability, while OPLS-DA model effectively distinguished the pairwise comparison samples, revealing 23 differential polyphenols with VIP scores >1 and P-value <0.05. OPLS model further revealed pronounced disparities in the polyphenol transfer from kernels to oils, indicating that FP were the primary drivers at lower shell ratios, while BP emerged as key contributors at higher ratios. These insights establish a scientific foundation for understanding the natural polyphenol transfer mechanisms in C. oleifera seeds, and contribute guidance for developing strategies for polyphenol retention and modulation during processing.PMID:40037042 | DOI:10.1016/j.foodchem.2025.143526

J Clin Endocrinol Metab. 2025 Mar 1:dgaf142. doi: 10.1210/clinem/dgaf142. Online ahead of print.ABSTRACTCONTEXT: While increased fiber intake may benefit appetite and metabolism in the general population, its effects in individuals with Prader-Willi Syndrome (PWS), a condition characterized by hyperphagia, obesity and metabolic dysregulation, remain to be explored.OBJECTIVES: This study assessed the effects of a fiber intervention on hyperphagia, metabolic health, and gut microbiota in individuals with PWS, and explored associations between changes in health markers and shifts in microbiota.METHODS: Participants received either a high-dose fiber intervention (35g/day) or a control for 3 weeks. Following a washout period of 4 to 8 weeks, participants switched treatments for another 3 weeks. Fecal (bacterial 16S ribosomal RNA) and blood (immunometabolic markers, targeted metabolomics) samples were collected before and after each treatment.RESULTS: Fourteen participants (with a median age of 13.6 years, 8 [57.1%] were female) reported high tolerance to the fiber intervention. While it did not significantly alter hyperphagia or key metabolic markers, the fiber intervention led to shifts in gut microbiota diversity and increased the abundance of beneficial bacteria, such as Bifidobacterium longum and Faecalibacterium prausnitzii. Additionally, it altered fecal and serum metabolites, including a decrease in branched-chain fatty acids and an increase in serum C4-OH acylcarnitine.CONCLUSION: While this study did not observe significant changes in primary or secondary endpoints, it suggests that a short-term high-fiber intervention may induce beneficial shifts in gut microbiota and microbial metabolites in individuals with PWS. Further research is warranted to investigate the long-term effects and potential therapeutic applications of fiber interventions in PWS.PMID:40036959 | DOI:10.1210/clinem/dgaf142

Nutr Rev. 2025 Mar 2:nuaf027. doi: 10.1093/nutrit/nuaf027. Online ahead of print.ABSTRACTThe dynamic balance between pro- and anti-inflammatory networks decreases as individuals age, and intestinal dysbiosis can initiate and maintain low-grade systemic inflammation. Interactions between the microbiota and humans occur from the beginning of life and, in general, the diversity of microbiota decreases with aging. The microbiome produces different metabolites with systemic effects, including immune system regulation. This understanding will be useful in controlling inflammation and preventing metabolic changes. Therefore, this review aims to identify the main metabolites synthesized by the intestinal microbiota to be used as biomarkers associated with longevity. This is a narrative review using scientific articles published in the last 10 years in the following databases: PubMed, Scielo, and Lilacs, using the Boolean operators "and" or "or." For this review, we identified 5 articles. The main metabolites described in the literature to date are organic acids, bile acids (BAs), short-chain fatty acids, branched-chain amino acids, trimethylamine N-oxide (TMAO), and derivatives of tryptophan and indole. Among these, the only ones not yet well characterized in studies on longevity were BAs and TMAO. Glutamate and p-cresol were also highlighted in the literature, with a negative association with longevity. The others showed an association, mostly positive, and can be used as potential biomarkers correlated with healthy aging and, if better studied, as targets for intervention to promote health and well-being.PMID:40036950 | DOI:10.1093/nutrit/nuaf027

Environ Toxicol Chem. 2025 Mar 1:vgaf056. doi: 10.1093/etojnl/vgaf056. Online ahead of print.ABSTRACTThe experimental design of New Approach Methodologies (NAMs) might deviate from common ecotoxicological studies, often requiring tailored statistical approaches. For instance, in NAMs developed for the detection of endocrine activity using aquatic vertebrate eleutheroembryos (Xenopus Eleutheroembryonic Thyroid Assay (XETA), Rapid Androgen Disruption Activity Reporter (RADAR) assay and Rapid Estrogen Activity In Vivo (REACTIV) assay), all concentration groups are nested within three independent study repeats, named 'runs' in the relevant Test Guidelines. Here, runs are referred to as replicates to emphasize their role as the repeated, independent entity. By contrast, for most other ecotoxicological studies the replicates are nested in the concentration groups. This leads to a different dependency structure for the XETA, RADAR and REACTIV assays. Disregarding this violates the basic statistical requirement for independence of observations potentially leading to incorrect conclusions. Unfortunately, in the statistical sections of the Test Guidelines of the XETA, RADAR and REACTIV assay, it is not clearly recommended to regard this dependency structure as statistical recommendations using a mixed ANOVA are provided only in the annexes. Here, we present "xeredar", an open-source R-package allowing automated statistical analysis of XETA, RADAR and REACTIV assays where the dependency structure of the data is correctly regarded through a mixed ANOVA. xeredar was validated on 36 XETA ring test studies and further tested on 41 RADAR ring test studies. A power analysis was carried out for the REACTIV assay, demonstrating that ignoring the dependency structure potentially leads to lower power and an increased false positive rate in comparison to the mixed ANOVA approach. The open-source R-package "xeredar" also comes with a Shiny app, making it accessible to everyone and thereby enhancing standardization and reproducibility for the statistical analyses of XETA, RADAR, and REACTIV assays.PMID:40036949 | DOI:10.1093/etojnl/vgaf056

J Proteome Res. 2025 Mar 4. doi: 10.1021/acs.jproteome.4c00795. Online ahead of print.ABSTRACTA nanosheath-flow capillary electrophoresis mass spectrometry (CE-MS) system with electrospray ionization was used to profile cationic metabolite cargo in exosomes secreted by nontumorigenic MCF-10A and tumorigenic MDA-MB-231 breast epithelial cells. An in-house-produced sheath liquid interface was developed and machined from PEEK to enable nanoflow volumes. Normalization of CE-MS peak areas to the total UV signal was employed to enhance quantitative accuracy and reduce variability. CE-MS-based metabolomics revealed increased purine synthesis intermediates and increased carnitine synthesis metabolites in MDA-MB-231-derived exosomes, with pathway enrichment indicating the activation of de novo purine pathways and upregulation of carnitine metabolism. In addition, nano-LC-MS-based proteomics revealed differential expression of ecto-5'-nucleotidase (NT5E) and mitochondrial aldehyde dehydrogenase (ALDH9A1), demonstrating metabolic alterations in related enzymatic steps. This study demonstrates the application of nanosheath-flow CE-MS for comprehensive and quantitative exosome metabolomics, uncovering metabolic reprogramming in purine and carnitine pathways between normal and cancerous breast cell lines and providing insight into exosome-mediated signaling of breast cancer metabolism.PMID:40036676 | DOI:10.1021/acs.jproteome.4c00795

Br J Dermatol. 2025 Feb 27:ljaf001. doi: 10.1093/bjd/ljaf001. Online ahead of print.ABSTRACTBACKGROUND: Prognosis and quality of life of advanced cutaneous T cell lymphoma (CTCL) patients, in particular those with Sézary syndrome (SS) and advanced-stage mycosis fungoides (MF), are poor. Monoclonal antibodies or antibody-drug conjugates (ADCs) have been implemented into CTCL therapy algorithms, but the spectrum of antibody-targetable cell-surface antigens on T cell non-Hodgkin lymphomas (T-NHL) is limited.OBJECTIVES: To evaluate expression of the MHC-II chaperone CD74 across common subtypes of CTCL by various methods, and to explore the efficacy of CD74-targeting of CTCL cells by anti-CD74 antibody-drug conjugate (ADC) in vitro and in vivo.METHODS: We comprehensively investigate expression of CD74 in well-defined CTCL cell lines by PCR analyses, immunoblotting and flow cytometry. More than 140 primary CTCL samples of all common entities are analyzed by immunohistochemistry, flow cytometry, immunofluorescence and 'co-detection by indexing' (CODEX) multiplexed tissue imaging as well as single-cell RNAseq analyses. DNA methylation of CTCL cell lines is interrogated by generation of genome-wide methylation profiling. The effect of a maytansinoid-conjugated humanized ADC against CD74 is investigated on CTCL cell lines in vitro, alone or in combination with gemcitabine, and in vivo after xenotransplantation of CTCL cell lines in NOD-scid Il2rgnull (NSG) mice.RESULTS: We demonstrate by different experimental approaches in CTCL cell lines and a broad collection of primary CTCL samples that CD74 is widely and robustly expressed in CTCL cells. Additionally, CD74 expression in SS and MF is confirmed by analyses of single cell (sc)RNA-seq data, and correlates in CTCL cell lines with CD74 gene DNA hypomethylation. CD74 is rapidly internalized in CTCL cells, and CD74 targeting by the ADC STRO-001 efficiently kills CTCL-derived cell lines. Finally, CD74 targeting synergizes with conventional chemotherapy in vitro, and eradicates murine xenotransplants of CTCL cell lines in vivo.CONCLUSIONS: CD74 is expressed across common CTCL subtypes, and CD74-targeting efficiently kills CTCL cells in vitro and in vivo. Our data thus identify CD74-targeting as highly promising treatment strategy for CTCL.PMID:40036608 | DOI:10.1093/bjd/ljaf001

Anal Chem. 2025 Mar 4. doi: 10.1021/acs.analchem.4c06682. Online ahead of print.ABSTRACTAchyrocline satureioides have good therapeutic effects on nonsmall cell lung cancer (NSCLC). Nevertheless, it is still challenging to elucidate the active ingredients and mechanism of action due to their complex chemical composition. To address this, we innovatively combined network pharmacology with spatial metabolomics to comprehensively investigate the active components and the action mechanism in the present study. First, metabolomics of cells treated with the methanol extract of A. satureioides (ASM) utilizing high-resolution ultrahigh-performance liquid chromatography tandem mass spectrometry (HR-UHPLC-MS/MS) revealed 32 changed metabolites and 7 enriched metabolic pathways, confirming the anti-NSCLC effect of ASM and its impact on endogenous metabolites at the cellular level. Then, 69 chemical components in the ASM were identified using HR-UHPLC-MS/MS, followed by the screening of 6 core components and 10 core targets of anti-NSCLC with the help of network pharmacology and molecular docking. Lastly, quercetin, the most abundant compound among the six core active ingredients, was chosen for evaluating its anti-NSCLC effect and the potential mechanism using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). 51 altered endogenous metabolites were screened, and pathway enrichment analysis results were consistent with cell metabolomics, corroborating our network pharmacology predictions. In addition, we also observed the accumulation of three metabolites of quercetin in the tumor tissues. Network pharmacology combined with MSI elucidated the metabolic mechanisms by which A. satureioides treats NSCLC, offering new insights into herbal cancer therapies.PMID:40036484 | DOI:10.1021/acs.analchem.4c06682

J Chem Inf Model. 2025 Mar 4. doi: 10.1021/acs.jcim.4c02212. Online ahead of print.ABSTRACTPredicting blood-brain barrier (BBB) penetration is crucial for developing central nervous system (CNS) drugs, representing a significant hurdle in successful clinical phase I studies. One of the most valuable properties for this prediction is the polar surface area (PSA). However, molecular structures are missing geometric optimization, which, together with lack of standardization, leads to variations in calculation. Additionally, prediction rules have been established by combining different molecular properties such as the BBB score or CNS multiparameter optimization (CNS MPO). This study aims to create an approach for 3D PSA calculation, to directly apply this value in combination with a set of 23 other parameters in a novel machine learning (ML)-based scoring, and to further evaluate existing prediction models using a standardized database. We developed and analyzed a standardized data set derived from the same laboratory, encompassing 24 calculated and experimentally determined molecular parameters such as PSA from various models, HPLC log P values, and hydrogen bond characteristics for 154 radiolabeled molecules and licensed or well-characterized drugs. These molecules were classified into categories based on BBB penetration, nonpenetration, and interactions with efflux transporters. We supplemented these with a novel in silico 3D calculation of nonclassical PSA. Additionally, we have calculated published prediction rules based on this standardized and transparent database. Using these data, we trained various ML models within a 100-fold Monte Carlo cross-validation framework to derive a novel ML-based prediction score for BBB penetration and validated the three most used existing predictive rules. To interpret the influence of individual molecular parameters and different existing predictive rules, we employed explainable artificial intelligence methods including Shapley additive explanations (SHAP) and surrogate modeling. The ML approach outperformed existing scores for BBB penetration by applying a complex nonlinear integration of molecular properties, with the random forest model achieving the best performance for predicting binary BBB penetration (area under the receiver operating characteristic curve (AUC) 0.88, 95% confidence intervals: 0.87-0.90), and multiclass efflux transporter versus CNS-positive and CNS-negative prediction (AUC 0.82, 95% CI: 0.81-0.82). SHAP analysis revealed the multifactorial nature of the problem, highlighting the advantage of multivariate models over single predictive parameters. The ML model's superior predictive capability was demonstrated in comparison with existing scoring systems, like the CNS MPO (AUC 0.53), the CNS MPO Positron emission tomography (PET) (AUC 0.51), and BBB score (AUC 0.68) while also enabling the identification of efflux transporter substrates and inhibitors. Our integrated ML approach, combining experimental and in silico measurements with novel in silico methods based on a standardized database including a plethora of different substance groups (licensed drugs and in vivo evaluated PET tracers), enhances the prediction of BBB penetration. This approach may reduce the reliance on extensive experimental measurements and animal testing, accelerating CNS drug development.PMID:40036481 | DOI:10.1021/acs.jcim.4c02212