PubMed

Comb Chem High Throughput Screen. 2023 May 4. doi: 10.2174/1386207326666230504124030. Online ahead of print.ABSTRACTINTRODUCTION: Cervical cancer is one of the malignant cancers with high mortality among women worldwide. Although vaccines and early detection have reduced cervical cancer mortality, it remains a malignancy with a high mortality rate in women.OBJECTIVE: We aimed to develop a novel integrated strategy that combines metabolomics with network pharmacology to explore the therapeutic mechanisms of naringin in cervical cancer. The mechanism of naringin intervention in cervical cancer was initially clarified by metabolomics and network pharmacology.METHODS: The method of LC-MS and network pharmacology for the detection and identification of potential biomarkers and the mechanisms of action of naringin was used. The metabolites were detected and identified based on ultra-high-performance liquid chromatography coupled with Quadrupole-Exactive Orbitrap MS (UHPLC-Q-Exactive Orbitrap MS) and followed by the network pharmacology analysis.RESULTS: In network pharmacology, naringin played a synergetic role through regulatory shared pathways, such as steroid hormone biosynthesis, sphingolipid signaling pathway and arachidonic acid metabolism, etc. Besides, the metabolomics analysis showed that 20 differential metabolites and 10 metabolic pathways were mainly involved in the therapeutic effect of naringin on cervical cancer. The result showed that naringin treatment for cervical cancer mainly occurs through the following metabolic pathways: amino acid metabolism and arachidonic acid metabolism.CONCLUSION: This work provided valuable information and a scientific basis for further studies of naringin in the treatment of cervical cancer.PMID:37143280 | DOI:10.2174/1386207326666230504124030

J Biol Chem. 2023 May 2:104774. doi: 10.1016/j.jbc.2023.104774. Online ahead of print.ABSTRACTMitochondria are signaling organelles implicated in cancer, but the mechanisms are elusive. Here, we show that Parkin, an E3 ubiquitin ligase altered in Parkinson's Disease (PD), forms a complex with the regulator of cell motility, Kindlin-2 (K2) at mitochondria of tumor cells. In turn, Parkin ubiquitinates Lys581 and Lys582 using Lys48 linkages, resulting in proteasomal degradation of K2 and shortened half-life from ∼5 h to ∼1.5 h. Loss of K2 inhibits focal adhesion turnover and β1 integrin activation, impairs membrane lamellipodia size and frequency, and inhibits mitochondrial dynamics, altogether suppressing tumor cell-ECM interactions, migration, and invasion. Conversely, Parkin does not affect tumor cell proliferation, cell cycle transitions or apoptosis. Expression of a Parkin ubiquitination-resistant K2 Lys581Ala/Lys582Ala double mutant is sufficient to restore membrane lamellipodia dynamics, correct mitochondrial fusion/fission, and preserve single-cell migration and invasion. In a 3D model of mammary gland developmental morphogenesis, impaired K2 ubiquitination drives multiple oncogenic traits of EMT, increased cell proliferation, reduced apoptosis and disrupted basal-apical polarity. Therefore, deregulated K2 is a potent oncogene and its ubiquitination by Parkin enables mitochondria-associated metastasis suppression.PMID:37142218 | DOI:10.1016/j.jbc.2023.104774

Environ Pollut. 2023 May 2:121766. doi: 10.1016/j.envpol.2023.121766. Online ahead of print.ABSTRACTLow dissolved oxygen (LO) in seawater negatively affects aquatic animals and has received considerable attention. However, there is still much to learn about how echinoderms, which are keystone species in benthic ecosystems, respond to hypoxic stress. Here, we detected differentially expressed metabolites (DEMs) in sea cucumber (Apositchopus japonicus) between normoxic conditions (NC group) and hypoxic conditions (2 mg L-1) for 3 and 7 days (i.e., LO3 and LO7 groups). A total of 156, 180, and 95 DEMs were found in the NC versus LO3, NC vs. LO7, and LO3 vs. LO7 comparisons, respectively. Amino acids were the most abundant class of DEMs, and "biosynthesis of amino acids" was an enriched pathway in all three comparisons. Most of the enriched metabolite sets under hypoxic stress were related to metabolism. As the duration of the hypoxia treatment extended, the metabolism-related process maintained an upward trend, and signaling pathways maintained a downward trend. Thus, metabolism-related processes are affected in hypoxia-stressed sea cucumber, and amino acid metabolism is the most important process for adaption to hypoxic conditions, potentially function in osmotic regulation and energy regulation. Our results shed light on the adaptative strategies of sea cucumber to challenging environmental conditions.PMID:37142211 | DOI:10.1016/j.envpol.2023.121766

J Ethnopharmacol. 2023 May 2:116557. doi: 10.1016/j.jep.2023.116557. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: The traditional Chinese herbal formula, Xiang-lian Pill (XLP), is commonly prescribed for ulcerative colitis (UC) patients to relieve their clinical symptom. Nonetheless, the underlying cellular and molecular mechanisms of XLP's anti-UC effect remain incompletely understood.AIM OF THE STUDY: To evaluate the therapeutic effect and elucidate the possible working mechanisms of XLP in UC treatment. The major active component of XLP was also characterized.MATERIALS AND METHODS: Colitis was induced in C57BL/6 mice with 3% dextran sulfate sodium (DSS) dissolved in drinking water for 7 consecutive days. The UC mice were grouped and treated with XLP (3640 mg/kg) or vehicle orally during the procedure of DSS induction. Mouse body weight, disease activity index (DAI) score and colon length were recorded. Histopathological changes and inflammatory cell infiltration were evaluated by pathological staining and flow cytometric analysis (FACS). Network pharmacology, bioinformatic analysis, widely targeted and targeted metabolomics analysis were performed to screen the potential effective ingredients and key targets. Bone marrow derived macrophages (BMDMs), peripheral blood mononuclear cells (PBMCs), RAW264.7 and THP-1 cells were used to dissect the anti-inflammatory effect of XLP.RESULTS: Oral administration of XLP ameliorated DSS induced mouse colitis, as evidenced by reduced DAI and colonic inflammatory destruction. FACS results demonstrated that XLP treatment effectively restored immune tolerance in colon, inhibited the generation of monocyte derived macrophages and skewed macrophage polarization into M2 phenotype. Network pharmacology analysis suggested that innate effector modules related to macrophage activation comprise the major targets of XLP, and the counter-regulatory STAT1/PPARγ signaling possibly serves as the critical downstream pathway. Subsequent experiments unveiled an imbalance of STAT1/PPARγ signaling in monocytes derived from UC patients, and validated that XLP suppressed LPS/IFN-γ induced macrophage activation (STAT1 mediated) but facilitated IL-4 induced macrophage M2 polarization (PPARγ dependent). Meanwhile, our data showed that quercetin served as the major component of XLP to recapitulate the regulatory effect on macrophages.CONCLUSION: Our findings revealed that quercetin serves as the major component of XLP that regulates macrophage alternative activation via tipping the balance of STAT1/PPARγ, which provides a mechanistic explanation for the therapeutic effect of XLP in UC treatment.PMID:37142141 | DOI:10.1016/j.jep.2023.116557

Sci Total Environ. 2023 May 2:163889. doi: 10.1016/j.scitotenv.2023.163889. Online ahead of print.ABSTRACTSalinity and heavy metal pollution seriously affect plant growth. Tamarix hispida (T. hispida) has the potential to remediate soil saline-alkali and heavy metal pollution. In this study, the response mechanisms of T. hispida under NaCl, CdCl2 (Cd) and combined CdCl2 and NaCl (Cd-NaCl) stresses were explored. Overall, the antioxidant system showed changes under the three stresses. The addition of NaCl inhibited the absorption of Cd2+. However, there were obvious differences in the transcripts and metabolites identified among the three stress responses. Interestingly, the number of DEGs was greatest under NaCl stress (929), but the number of differentially expressed metabolites (DEMs) was lowest (48), with 143 and 187 DEMs identified under Cd and Cd-NaCl stress, respectively. It is worth noting that both DEGs and DEMs were enriched in the linoleic acid metabolism pathway under Cd stress. In particular, the content of lipids changed significantly under Cd and Cd-NaCl stress, suggesting that maintaining normal lipid synthesis and metabolism may be an important way to improve the Cd tolerance of T. hispida. Flavonoids may also play an important role in the response to NaCl and Cd stress. These results provide a theoretical basis for cultivating plants with improved salt and cadmium repair abilities.PMID:37142042 | DOI:10.1016/j.scitotenv.2023.163889

Poult Sci. 2023 Apr 12;102(7):102718. doi: 10.1016/j.psj.2023.102718. Online ahead of print.ABSTRACTApproaches for the diagnosis of wooden breast (WB) myopathy in live birds are urgently required before applying intervention strategies to reduce occurrence and severity for the poultry industry. The objective of this study was to characterize the serum metabolic profiles in male broilers affected by WB and to identify biomarkers related to this myopathy. Broilers were categorized into normal (CON) and WB groups based on gross scoring and histological evaluation. Gas chromatography-mass spectrometry-based metabolomics, multivariate analysis, and orthogonal partial least squares discriminant analysis revealed a clear separation between CON and WB. A total of 73 significantly different (P < 0.05) metabolites with 17 upregulated and 56 downregulated were identified, which were mainly involved in pathways of alanine, aspartate, and glutamate metabolism, carbohydrate metabolism, and taurine and hypotaurine metabolism. By using the nested cross-validation function of random forest analysis, 9 significantly altered (P < 0.05) metabolites (cerotinic acid, arabitol, phosphoenolpyruvate, terephthalic acid, cis-gondoic acid, N-acetyl-d-glucosamine, 4-hydroxymandelic acid, caffeine, and xanthurenic acid) were identified as biomarkers with an excellent discriminant performance for WB myopathy. Collectively, this study provides new insights for a deeper understanding of the pathogenesis and provides metabolites as biomarkers for diagnostic utilization of WB myopathy.PMID:37141813 | DOI:10.1016/j.psj.2023.102718

J Magn Reson. 2023 Apr 26;352:107462. doi: 10.1016/j.jmr.2023.107462. Online ahead of print.ABSTRACTNMR is a key technology for metabolomics because of its robustness and reproducibility. Herein we discuss practical considerations that extend the utility of NMR spectroscopy. First, the long T1 spin relaxation times of small molecules limits high-throughput data acquisition because most experimental time is lost while waiting for signal recovery. In principle, the addition of a small amount of commercially-available paramagnetic gadolinium chelate allows cost-effective and efficient high-throughput mixture analysis with correct concentration determination. However, idle time caused by slow temperature regulation during sample exchanges, poses a next constraint. We show how, with proper care, NMR sample scanning times can be reduced additionally by a factor of two. Lastly, we describe how equidistant bucketing is a simple and fast procedure for metabolomic fingerprinting. The combination of these advancements help to make NMR metabolomics more versatile than it is today.PMID:37141802 | DOI:10.1016/j.jmr.2023.107462

Semin Immunol. 2023 May 2;67:101767. doi: 10.1016/j.smim.2023.101767. Online ahead of print.NO ABSTRACTPMID:37141767 | DOI:10.1016/j.smim.2023.101767

Food Chem. 2023 Apr 28;422:136231. doi: 10.1016/j.foodchem.2023.136231. Online ahead of print.ABSTRACTAn integrated metabolomics approach based on UPLC-QTOF-MS and HS-SPME-GC-orbitrap-MS was performed to investigate the dynamic changes of metabolite profiling in chickpeas, red speckled kidney beans, and mung beans during soaking. There were 23, 23, 16 non-volatile metabolites, and 18, 21, 22 volatile metabolites were identified as differential metabolites in chickpeas, red speckled kidney beans, and mung beans during soaking, respectively. These metabolites mainly included flavonoids, lysophosphatidylcholines (LPCs), lysophosphatidylethanolamines (LPEs), fatty acids, alcohols, aldehydes, and esters. The key time points responsible for the significant changes in metabolites and quality of the three pulses were 4, 8, and 24 h of soaking. Results revealed that the variations of some metabolites could attribute to oxidation and hydrolysis reactions. These results contribute to a better understanding of how soaking affects pulses quality, and provide useful information for determining soaking time according to nutritional and sensory requirements of their final products or dishes.PMID:37141754 | DOI:10.1016/j.foodchem.2023.136231

Trials. 2023 May 4;24(1):308. doi: 10.1186/s13063-023-07317-w.ABSTRACTBACKGROUND: Major depressive disorder (MDD) with atypical features, namely depression with atypical features (AFD), is one of the most common clinical specifiers of MDD, closely associated with bipolar disorder (BD). However, there is still a lack of clinical guidelines for the diagnosis, treatment, and prognosis of AFD. Our study mainly focuses on three issues about how to identify AFD, what is the appropriate individualized treatment for AFD, and what are the predictive biomarkers of conversion to BD.METHODS: The Study of Individualized Diagnosis and Treatment for Depression with Atypical Features (iDoT-AFD) is a multicenter, prospective, open-label study consisting of a 12-week randomized controlled trial (RCT) and a continued follow-up until 4 years or reaching the study endpoint. It is enrolling 480 patients with AFD (120 per treatment arm), 100 patients with BD, and 100 healthy controls (HC). Multivariate dimension information is collected including clinical features, cognitive function, kynurenine pathway metabolomics, and multimodal magnetic resonance imaging (MRI) data. Firstly, multivariate informatics analyses are performed to recognize patients with AFD from participants including the first-episode and recurrent atypical depression, patients with BD, and patients with HC. Secondly, patients with atypical depression are randomly allocated to one of the four treatment groups including "single application of selective serotonin reuptake inhibitor (SSRI) or serotonin-noradrenaline reuptake inhibitor (SNRI)", "SSRI/SNRI combined with mood stabilizer," "SSRI/SNRI combined with quetiapine (≥ 150 mg/day)," or "treatment as usual (TAU)" and then followed up 12 weeks to find out the optimized treatment strategies. Thirdly, patients with atypical depression are followed up until 4 years or switching to BD, to explore the risk factors of conversion from atypical depression to BD and eventually build the risk warning model of conversion to BD.DISCUSSION: The first enrolment was in August 2019. The iDoT-AFD study explores the clinical and biological markers for the diagnosis, treatment, and prognosis of AFD and further provides evidence for clinical guidelines of AFD.TRIAL REGISTRATION: ClinicalTrials.gov NCT04209166. Registered on December 19, 2019.PMID:37143128 | DOI:10.1186/s13063-023-07317-w

Chin Med. 2023 May 4;18(1):48. doi: 10.1186/s13020-023-00750-8.ABSTRACTBACKGROUND: Cold-dampness Syndrome (RA-Cold) and Hot-dampness Syndrome (RA-Hot) are two distinct groups of rheumatoid arthritis (RA) patients with different clinical symptoms based on traditional Chinese medicine (TCM) theories and clinical empirical knowledge. However, the biological basis of the two syndromes has not been fully elucidated, which may restrict the development of personalized medicine and drug discovery for RA diagnosis and therapy.METHODS: An integrative strategy combining clinical transcriptomics, phenomics, and metabolomics data based on clinical cohorts and adjuvant-induced arthritis rat models was performed to identify novel candidate biomarkers and to investigate the biological basis of RA-Cold and RA-Hot.RESULTS: The main clinical symptoms of RA-Cold patients are joint swelling, pain, and contracture, which may be associated with the dysregulation of T cell-mediated immunity, osteoblast differentiation, and subsequent disorders of steroid biosynthesis and phenylalanine metabolism. In contrast, the main clinical symptoms of RA-Hot patients are fever, irritability, and vertigo, which may be associated with various signals regulating angiogenesis, adrenocorticotropic hormone release, and NLRP3 inflammasome activation, leading to disorders of steroid biosynthesis, nicotinamide, and sphingolipid metabolism. IL17F, 5-HT, and IL4I1 were identified as candidate biomarkers of RA-Cold, while S1P and GLNS were identified as candidate biomarkers of RA-Hot.CONCLUSIONS: The current study presents the most comprehensive metabonomic and transcriptomic profiling of serum, urine, synovial fluid, and synovial tissue samples obtained from RA-Cold and RA-Hot patients and experimental animal models to date. Through the integration of multi-omics data and clinical independent validation, a list of novel candidate biomarkers of RA-Cold and RA-Hot syndromes were identified, that may be useful in improving RA diagnosis and therapy.PMID:37143094 | DOI:10.1186/s13020-023-00750-8

Methods Mol Biol. 2023;2644:193-209. doi: 10.1007/978-1-0716-3052-5_12.ABSTRACTCellular health, functionality, response to environment, and other variables affecting cell, tissue, or organ viability are reflected in the cellular proteomes and metabolomes. These "omic" profiles are in constant flux even during normal cellular functioning, to maintain cellular homeostasis, in response to small environmental changes and maintenance of optimal cell viability. However proteomic "fingerprints" can also provide insight into cellular ageing, response to disease, adjustment to environmental changes, and other variables that impact cellular viability. A variety of proteomic methods can be used to determine qualitative and quantitative proteomic change. In this chapter, we will focus on a labeling method called isobaric tags for relative and absolute quantification (iTRAQ), which is frequently used to identify and quantify proteomic expression changes in cells and tissues.PMID:37142923 | DOI:10.1007/978-1-0716-3052-5_12

Cell Death Dis. 2023 May 5;14(5):306. doi: 10.1038/s41419-023-05806-z.ABSTRACTThe major underlying cause for the high mortality rate in colorectal cancer (CRC) relies on its drug resistance, to which intratumor heterogeneity (ITH) contributes substantially. CRC tumors have been reported to comprise heterogeneous populations of cancer cells that can be grouped into 4 consensus molecular subtypes (CMS). However, the impact of inter-cellular interaction between these cellular states on the emergence of drug resistance and CRC progression remains elusive. Here, we explored the interaction between cell lines belonging to the CMS1 (HCT116 and LoVo) and the CMS4 (SW620 and MDST8) in a 3D coculture model, mimicking the ITH of CRC. The spatial distribution of each cell population showed that CMS1 cells had a preference to grow in the center of cocultured spheroids, while CMS4 cells localized at the periphery, in line with observations in tumors from CRC patients. Cocultures of CMS1 and CMS4 cells did not alter cell growth, but significantly sustained the survival of both CMS1 and CMS4 cells in response to the front-line chemotherapeutic agent 5-fluorouracil (5-FU). Mechanistically, the secretome of CMS1 cells exhibited a remarkable protective effect for CMS4 cells against 5-FU treatment, while promoting cellular invasion. Secreted metabolites may be responsible for these effects, as demonstrated by the existence of 5-FU induced metabolomic shifts, as well as by the experimental transfer of the metabolome between CMS1 and CMS4 cells. Overall, our results suggest that the interplay between CMS1 and CMS4 cells stimulates CRC progression and reduces the efficacy of chemotherapy.PMID:37142595 | DOI:10.1038/s41419-023-05806-z

Nat Commun. 2023 May 4;14(1):2581. doi: 10.1038/s41467-023-38335-6.ABSTRACTMany signaling and other genes known as "hidden" drivers may not be genetically or epigenetically altered or differentially expressed at the mRNA or protein levels, but, rather, drive a phenotype such as tumorigenesis via post-translational modification or other mechanisms. However, conventional approaches based on genomics or differential expression are limited in exposing such hidden drivers. Here, we present a comprehensive algorithm and toolkit NetBID2 (data-driven network-based Bayesian inference of drivers, version 2), which reverse-engineers context-specific interactomes and integrates network activity inferred from large-scale multi-omics data, empowering the identification of hidden drivers that could not be detected by traditional analyses. NetBID2 has substantially re-engineered the previous prototype version by providing versatile data visualization and sophisticated statistical analyses, which strongly facilitate researchers for result interpretation through end-to-end multi-omics data analysis. We demonstrate the power of NetBID2 using three hidden driver examples. We deploy NetBID2 Viewer, Runner, and Cloud apps with 145 context-specific gene regulatory and signaling networks across normal tissues and paediatric and adult cancers to facilitate end-to-end analysis, real-time interactive visualization and cloud-based data sharing. NetBID2 is freely available at https://jyyulab.github.io/NetBID .PMID:37142594 | DOI:10.1038/s41467-023-38335-6

Nat Commun. 2023 May 4;14(1):2587. doi: 10.1038/s41467-023-38304-z.ABSTRACTMulti-enzymatic cascades with enzymes arranged in close-proximity through a protein scaffold can trigger a substrate channeling effect, allowing for efficient cofactor reuse with industrial potential. However, precise nanometric organization of enzymes challenges the design of scaffolds. In this study, we create a nanometrically organized multi-enzymatic system exploiting engineered Tetrapeptide Repeat Affinity Proteins (TRAPs) as scaffolding for biocatalysis. We genetically fuse TRAP domains and program them to selectively and orthogonally recognize peptide-tags fused to enzymes, which upon binding form spatially organized metabolomes. In addition, the scaffold encodes binding sites to selectively and reversibly sequester reaction intermediates like cofactors via electrostatic interactions, increasing their local concentration and, consequently, the catalytic efficiency. This concept is demonstrated for the biosynthesis of amino acids and amines using up to three enzymes. Scaffolded multi-enzyme systems present up to 5-fold higher specific productivity than the non-scaffolded ones. In-depth analysis suggests that channeling of NADH cofactor between the assembled enzymes enhances the overall cascade throughput and the product yield. Moreover, we immobilize this biomolecular scaffold on solid supports, creating reusable heterogeneous multi-functional biocatalysts for consecutive operational batch cycles. Our results demonstrate the potential of TRAP-scaffolding systems as spatial-organizing tools to increase the efficiency of cell-free biosynthetic pathways.PMID:37142589 | DOI:10.1038/s41467-023-38304-z

J Plant Physiol. 2023 Apr 27;285:153996. doi: 10.1016/j.jplph.2023.153996. Online ahead of print.ABSTRACTContinuous cropping of ginseng leads to serious declines in yield and quality because of self-toxicity of allelochemicals and other factors in soil. However, because of the long growth cycle and low survival rate of ginseng, rapid screening of autotoxic activity is difficult. Therefore, it is important to analyze the allelochemicals and identify a model plant with autotoxic responses similar to those of ginseng. In this study, UPLC-Orbitrap-HRMS targeted metabolomics and verification of autotoxic activity were used to analyze a problem soil from continuously cropped ginseng. Allelochemical markers were screened by OPLS-DA. Seeds and seedlings of maize, Chinese cabbage, cucumber, green beans, wheat, sunflower, and oats were selected to identify potential model plants. Model plants with autotoxic responses similar to those of ginseng were evaluated by comparing morphological, physiological, and biochemical characteristics. The n-butanol extract of the continuously cropped problem soil had the most significant autotoxic activity. Twenty-three ginsenosides and the contributions to autotoxic effects were screened and evaluated. Of potential model plants, seeds and seedlings of cucumber showed similar growth inhibition to that of ginseng under the action of allelochemicals. Thus, metabolomics can be used to screen allelochemicals in soil and predict the autotoxic effects, and the cucumber plant model can be used to rapidly screen allelopathic activity of ginseng. The study will provide reference for methodology in allelopathy research on ginseng.PMID:37141674 | DOI:10.1016/j.jplph.2023.153996

Biotechnol Prog. 2023 May 4:e3352. doi: 10.1002/btpr.3352. Online ahead of print.ABSTRACTThe strategy of temperature downshift has been widely used in the biopharmaceutical industry to improve antibody production and cell-specific production rate (qp ) with Chinese hamster ovary cells (CHO). However, the mechanism of temperature-induced metabolic rearrangement, especially important intracellular metabolic events, remains poorly understood. In this work, in order to explore the mechanisms of temperature-induced cell metabolism, we systematically assessed the differences in cell growth, antibody expression, and antibody quality between high-producing (HP) and low-producing (LP) CHO cell lines under both constant temperature (37°C) and temperature downshift (37°C→33°C) settings during fed-batch culture. Although the results showed that low-temperature culture during the late phase of exponential cell growth significantly reduced the maximum viable cell density (p < 0.05) and induced cell cycle arrest in the G0/G1 phase, this temperature downshift led to a higher cellular viability and increased antibody titer by 48% and 28% in HP and LP CHO cell cultures, respectively (p < 0.001), and favored antibody quality reflected in reduced charge heterogeneity and molecular size heterogeneity. Combined extra- and intra-cellular metabolomics analyses revealed that temperature downshift significantly downregulated intracellular glycolytic and lipid metabolic pathways while upregulated tricarboxylic acid (TCA) cycle, and particularly featured upregulated glutathione metabolic pathways. Interestingly, all these metabolic pathways were closely associated with the maintenance of intracellular redox state and oxidative stress-alleviating strategies. To experimentally address this, we developed two high-performance fluorescent biosensors, denoted SoNar and iNap1, for real-time monitoring of intracellular nicotinamide adenine dinucleotide/nicotinamide adenine dinucleotide + hydrogen (NAD+ /NADH) ratio and nicotinamide adenine dinucleotide phosphate (NADPH) amount, respectively. Consistent with such metabolic rearrangements, the results showed that temperature downshift decreased the intracellular NAD+ /NADH ratio, which might be ascribed to the re-consumption of lactate, and increased the intracellular NADPH amount (p < 0.01) to scavenge intracellular reactive oxygen species (ROS) induced by the increased metabolic requirements for high-level expression of antibody. Collectively, this study provides a metabolic map of cellular metabolic rearrangement induced by temperature downshift and demonstrates the feasibility of real-time fluorescent biosensors for biological processes, thus potentially providing a new strategy for dynamic optimization of antibody production processes.PMID:37141532 | DOI:10.1002/btpr.3352

Environ Health Perspect. 2023 May;131(5):57002. doi: 10.1289/EHP11139. Epub 2023 May 4.ABSTRACTBACKGROUND: Exposure to traffic-related air pollution (TRAP) has been associated with increased risks of respiratory diseases, but the biological mechanisms are not yet fully elucidated.OBJECTIVES: Our aim was to evaluate the respiratory responses and explore potential biological mechanisms of TRAP exposure in a randomized crossover trial.METHODS: We conducted a randomized crossover trial in 56 healthy adults. Each participant was exposed to high- and low-TRAP exposure sessions by walking in a park and down a road with high traffic volume for 4 h in random order. Respiratory symptoms and lung function, including forced expiratory volume in the first second (FEV1), forced vital capacity (FVC), the ratio of FEV1 to FVC, and maximal mid-expiratory flow (MMEF), were measured before and after each exposure session. Markers of 8-isoprostane, tumor necrosis factor-α (TNF-α), and ezrin in exhaled breath condensate (EBC), and surfactant proteins D (SP-D) in serum were also measured. We used linear mixed-effects models to estimate the associations, adjusted for age, sex, body mass index, meteorological condition, and batch (only for biomarkers). Liquid chromatography-mass spectrometry was used to profile the EBC metabolome. Untargeted metabolome-wide association study (MWAS) analysis and pathway enrichment analysis using mummichog were performed to identify critical metabolomic features and pathways associated with TRAP exposure.RESULTS: Participants had two to three times higher exposure to traffic-related air pollutants except for fine particulate matter while walking along the road compared with in the park. Compared with the low-TRAP exposure at the park, high-TRAP exposure at the road was associated with a higher score of respiratory symptoms [2.615 (95% CI: 0.605, 4.626), p=1.2×10-2] and relatively lower lung function indicators [-0.075L (95% CI: -0.138, -0.012), p=2.1×10-2] for FEV1 and -0.190L/s (95% CI: -0.351, -0.029; p=2.4×10-2) for MMEF]. Exposure to TRAP was significantly associated with changes in some, but not all, biomarkers, particularly with a 0.494-ng/mL (95% CI: 0.297, 0.691; p=9.5×10-6) increase for serum SP-D and a 0.123-ng/mL (95% CI: -0.208, -0.037; p=7.2×10-3) decrease for EBC ezrin. Untargeted MWAS analysis revealed that elevated TRAP exposure was significantly associated with perturbations in 23 and 32 metabolic pathways under positive- and negative-ion modes, respectively. These pathways were most related to inflammatory response, oxidative stress, and energy use metabolism.CONCLUSIONS: This study suggests that TRAP exposure might lead to lung function impairment and respiratory symptoms. Possible underlying mechanisms include lung epithelial injury, inflammation, oxidative stress, and energy metabolism disorders. https://doi.org/10.1289/EHP11139.PMID:37141245 | DOI:10.1289/EHP11139

PLoS One. 2023 May 4;18(5):e0284315. doi: 10.1371/journal.pone.0284315. eCollection 2023.ABSTRACTMachine learning (ML) models are used in clinical metabolomics studies most notably for biomarker discoveries, to identify metabolites that discriminate between a case and control group. To improve understanding of the underlying biomedical problem and to bolster confidence in these discoveries, model interpretability is germane. In metabolomics, partial least square discriminant analysis (PLS-DA) and its variants are widely used, partly due to the model's interpretability with the Variable Influence in Projection (VIP) scores, a global interpretable method. Herein, Tree-based Shapley Additive explanations (SHAP), an interpretable ML method grounded in game theory, was used to explain ML models with local explanation properties. In this study, ML experiments (binary classification) were conducted for three published metabolomics datasets using PLS-DA, random forests, gradient boosting, and extreme gradient boosting (XGBoost). Using one of the datasets, PLS-DA model was explained using VIP scores, while one of the best-performing models, a random forest model, was interpreted using Tree SHAP. The results show that SHAP has a more explanation depth than PLS-DA's VIP, making it a powerful method for rationalizing machine learning predictions from metabolomics studies.PMID:37141218 | DOI:10.1371/journal.pone.0284315

Angew Chem Int Ed Engl. 2023 May 4:e202302110. doi: 10.1002/anie.202302110. Online ahead of print.ABSTRACTHyperpolarized nuclear magnetic resonance (NMR) offers an ensemble of methods that remarkably address the sensitivity issues of NMR. Dissolution Dynamic Nuclear Polarization (d-DNP) provides a unique and general way to detect 13C NMR signals with a sensitivity enhanced by several orders of magnitude. The expanding application scope of d-DNP now encompasses the analysis of complex mixtures at natural 13C abundance. However, it has in this area been limited to metabolite extracts. Here, we report the first d-DNP-enhanced 13C NMR analysis of a biofluid -urine- at natural abundance, offering unprecedented resolution and sensitivity for this challenging type of sample. We also show that accurate quantitative information on multiple targeted metabolites can be retrieved through a standard addition procedure.PMID:37141160 | DOI:10.1002/anie.202302110