PubMed

Hemasphere. 2023 Apr 5;7(4):e858. doi: 10.1097/HS9.0000000000000858. eCollection 2023 Apr.ABSTRACTEarly fever after chimeric antigen receptor T-cell (CAR-T) therapy can reflect both an infection or cytokine release syndrome (CRS). Identifying early infections in the setting of CRS and neutropenia represents an unresolved clinical challenge. In this retrospective observational analysis, early fever events (day 0-30) were characterized as infection versus CRS in 62 patients treated with standard-of-care CD19.CAR-T for relapsed/refractory B-cell non-Hodgkin lymphoma. Routine serum inflammatory markers (C-reactive protein [CRP], interleukin-6 [IL-6], procalcitonin [PCT]) were recorded daily. Exploratory plasma proteomics were performed longitudinally in 52 patients using a multiplex proximity extension assay (Olink proteomics). Compared with the CRSonly cohort, we noted increased event-day IL-6 (median 2243 versus 64 pg/mL, P = 0.03) and particularly high PCT levels (median 1.6 versus 0.3 µg/L, P < 0.0001) in the patients that developed severe infections. For PCT, an optimal discriminatory threshold of 1.5 µg/L was established (area under the receiver operating characteristic curve [AUCROC] = 0.78). Next, we incorporated day-of-fever PCT levels with the patient-individual CAR-HEMATOTOX score. In a multicenter validation cohort (n = 125), we confirmed the discriminatory capacity of this so-called HT10 score for early infections at first fever (AUCROC = 0.87, P < 0.0001, sens. 86%, spec. 86%). Additionally, Olink proteomics revealed pronounced immune dysregulation and endothelial dysfunction in patients with severe infections as evidenced by an increased ANGPT2/1 ratio and an altered CD40/CD40L-axis. In conclusion, the high discriminatory capacity of the HT10 score for infections highlights the advantage of dynamic risk assessment and supports the incorporation of PCT into routine inflammatory panels. Candidate markers from Olink proteomics may further refine risk-stratification. If validated prospectively, the score will enable risk-adapted decisions on antibiotic use.PMID:37038465 | PMC:PMC10082278 | DOI:10.1097/HS9.0000000000000858

Cell Rep. 2023 Apr 10:112299. doi: 10.1016/j.celrep.2023.112299. Online ahead of print.ABSTRACTUnderstanding the axis of the human microbiome and physiological homeostasis is an essential task in managing deep-space-travel-associated health risks. The NASA-led Rodent Research 5 mission enabled an ancillary investigation of the gut microbiome, varying exposure to microgravity (flight) relative to ground controls in the context of previously shown bone mineral density (BMD) loss that was observed in these flight groups. We demonstrate elevated abundance of Lactobacillus murinus and Dorea sp. during microgravity exposure relative to ground control through whole-genome sequencing and 16S rRNA analyses. Specific functionally assigned gene clusters of L. murinus and Dorea sp. capable of producing metabolites, lactic acid, leucine/isoleucine, and glutathione are enriched. These metabolites are elevated in the microgravity-exposed host serum as shown by liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomic analysis. Along with BMD loss, ELISA reveals increases in osteocalcin and reductions in tartrate-resistant acid phosphatase 5b signifying additional loss of bone homeostasis in flight.PMID:37080202 | DOI:10.1016/j.celrep.2023.112299

BMC Plant Biol. 2023 Apr 10;23(1):190. doi: 10.1186/s12870-023-04195-x.ABSTRACTBACKGROUND: Waxy corn has a short growth cycle and high multiple cropping index. However, after being planted in early spring, late autumn and winter, it is susceptible to low temperature (LT), which reduces the emergence rate and yield. Therefore, it is important to analyze the response mechanism of waxy corn under LT stress.RESULTS: All phenotype indexes of waxy corn inbred lines N28 were significantly higher than waxy corn inbred lines N67 under LT. With the increase of LT stress time, all physiological indexes showed an upward trend in N28 and N67. Differentially expressed genes (DEGs) 16,017 and 14,435 were identified in N28 and N67 compared with nongerminated control under LT germination, respectively, and differential metabolites 127 and 93 were detected in N28 and N67, respectively. In addition, the expression level of some genes involved in plant hormones and mitogen activated protein kinase (MAPK) signaling pathways was significantly up-regulated in N28. Compared with N67, flavonoid metabolites were also significantly enriched in N28 under LT germination.CONCLUSION: Under LT stress, the inbred lines N28 was significantly higher than the inbred lines N67 in the phenotypic and physiological indices of cold resistance. Compared with N67, the expression levels of some genes involved in the plant hormones and MAPK pathways were significantly up-regulated in N28, and flavonoid metabolites were also significantly enriched in N28 under LT stress. These genes and metabolites may help N28 to improve cold resistance and may be as potential target genes for cold resistance breeding in waxy corn.PMID:37038118 | DOI:10.1186/s12870-023-04195-x

BMC Plant Biol. 2023 Apr 10;23(1):192. doi: 10.1186/s12870-023-04209-8.ABSTRACTBACKGROUND: As an important plant source of food and edible oils, pecans are rich in metabolites. Few studies have focused on metabolites involved in pecan seed germination at different temperatures.RESULTS: In our study, we germinated pecan seeds at different temperatures and found that, the germination rate and water content were highest at 30°C. It was found that the radicle of pecan seeds could sense seed coat cracking by observing the microstructure and cell ultra-structure of the seeds at the early stage of germination. We compared the metabolomes of seeds at different temperatures with different germination processes. A total of 349 metabolites were identified, including 138 primary metabolites and 211 secondary metabolites. KEGG enrichment analysis indicated that the differential metabolites were mainly enriched in the metabolic pathways, amino acid synthesis pathways and ABC transporters. Using weighted gene co-expression network analysis (WGCNA), three modules of closely related metabolites were identified. In the brown module, most of hub metabolites were amino substances, whereas in the blue module, many hub metabolites were sugars.CONCLUSIONS: Amino acids and carbohydrates play an important role in pecan seed germination. Differential metaboliteanalysis showed that 30°C was the temperature at which metabolites differed most significantly. This study provides useful information for further research on the seedling establishment of pecan seeds.PMID:37038116 | DOI:10.1186/s12870-023-04209-8

Adv Sci (Weinh). 2023 Apr 10:e2207454. doi: 10.1002/advs.202207454. Online ahead of print.ABSTRACTPulmonary fibrosis (PF) is a heterogeneous disease with a poor prognosis. Therefore, identifying additional therapeutic modalities is required to improve outcome. However, the lack of biomarkers of disease progression hampers the preclinical to clinical translational process. Here, this work assesses and identifies progressive alterations in pulmonary function, transcriptomics, and metabolomics in the mouse lung at 7, 14, 21, and 28 days after a single dose of oropharyngeal bleomycin. By integrating multi-omics data, this work identifies two central gene subnetworks associated with multiple critical pathological changes in transcriptomics and metabolomics as well as pulmonary function. This work presents a multi-omics-based framework to establish a translational link between the bleomycin-induced PF model in mice and human idiopathic pulmonary fibrosis to identify druggable targets and test therapeutic candidates. This work also indicates peripheral cannabinoid receptor 1 (CB1 R) antagonism as a rational therapeutic target for clinical translation in PF. Mouse Lung Fibrosis Atlas can be accessed freely at https://niaaa.nih.gov/mouselungfibrosisatlas.PMID:37038090 | DOI:10.1002/advs.202207454

Anal Sci. 2023 Apr 10. doi: 10.1007/s44211-023-00334-4. Online ahead of print.ABSTRACTThe quantitative analysis of near-infrared spectroscopy in traditional Chinese medicine has still deficiencies in the selection of the measured indexes. Then Paeoniae Radix Alba is one of the famous "Eight Flavors of Zhejiang" herbs, however, it lacks the pharmacodynamic support, and cannot reflect the quality of Paeoniae Radix Alba accurately and reasonably. In this study, the spectrum-effect relationship of the anti-inflammatory activity of Paeoniae Radix Alba was established. Then based on the obtained bioactive component groups, the genetic algorithm, back propagation neural network, was combined with near-infrared spectroscopy to establish calibration models for the content of the bioactive components of Paeoniae Radix Alba. Finally, three bioactive components, paeoniflorin, 1,2,3,4,6-O-pentagalloylglucose, and benzoyl paeoniflorin, were successfully obtained. Their near-infrared spectroscopy content models were also established separately, and the validation sets results showed the coefficient of determination (R2 > 0.85), indicating that good calibration statistics were obtained for the prediction of key pharmacodynamic components. As a result, an integrated analytical method of spectrum-effect relationship combined with near-infrared spectroscopy and deep learning algorithm was first proposed to assess and control the quality of traditional Chinese medicine, which is the future development trend for the rapid inspection of traditional Chinese medicine.PMID:37037970 | DOI:10.1007/s44211-023-00334-4

Mol Psychiatry. 2023 Apr 10. doi: 10.1038/s41380-023-02051-w. Online ahead of print.ABSTRACTThe discovery of prenatal and neonatal molecular biomarkers has the potential to yield insights into autism spectrum disorder (ASD) and facilitate early diagnosis. We characterized metabolomic profiles in ASD using plasma samples collected in the Norwegian Autism Birth Cohort from mothers at weeks 17-21 gestation (maternal mid-gestation, MMG, n = 408) and from children on the day of birth (cord blood, CB, n = 418). We analyzed associations using sex-stratified adjusted logistic regression models with Bayesian analyses. Chemical enrichment analyses (ChemRICH) were performed to determine altered chemical clusters. We also employed machine learning algorithms to assess the utility of metabolomics as ASD biomarkers. We identified ASD associations with a variety of chemical compounds including arachidonic acid, glutamate, and glutamine, and metabolite clusters including hydroxy eicospentaenoic acids, phosphatidylcholines, and ceramides in MMG and CB plasma that are consistent with inflammation, disruption of membrane integrity, and impaired neurotransmission and neurotoxicity. Girls with ASD have disruption of ether/non-ether phospholipid balance in the MMG plasma that is similar to that found in other neurodevelopmental disorders. ASD boys in the CB analyses had the highest number of dysregulated chemical clusters. Machine learning classifiers distinguished ASD cases from controls with area under the receiver operating characteristic (AUROC) values ranging from 0.710 to 0.853. Predictive performance was better in CB analyses than in MMG. These findings may provide new insights into the sex-specific differences in ASD and have implications for discovery of biomarkers that may enable early detection and intervention.PMID:37037873 | DOI:10.1038/s41380-023-02051-w

Phytother Res. 2023 Apr 10. doi: 10.1002/ptr.7827. Online ahead of print.ABSTRACTDiabetic cognitive impairment (DCI) is a serious neurodegenerative disorder caused by diabetes, with chronic inflammation being a crucial factor in its pathogenesis. Pterostilbene is a well-known natural stilbene derivative that has excellent anti-inflammatory activity, suggesting its potential medicinal advantages for treating DCI. Therefore, this study is to explore the beneficial effects of pterostilbene for improving cognitive dysfunction in DCI mice. A diabetic model was induced by a high-fat diet plus streptozotocin (40 mg·kg-1 ) for consecutive 5 days. After the animals were confirmed to be in a diabetic state, they were treated with pterostilbene (20 or 60 mg·kg-1 , i.g.) for 10 weeks. Pharmacological evaluation showed pterostilbene could ameliorate cognitive dysfunction, regulate glycolipid metabolism disorders, improve neuronal damage, and reduce the accumulation of β-amyloid in DCI mice. Pterostilbene alleviated neuroinflammation by suppressing oxidative stress and carbonyl stress damage, astrocyte and microglia activation, and dopaminergic neuronal loss. Further investigations showed that pterostilbene reduced the level of lipopolysaccharide, modulated colon and brain TLR4/NF-κB signaling pathways, and decreased the release of inflammatory factors, which in turn inhibited intestinal inflammation and neuroinflammation. Furthermore, pterostilbene could also improve the homeostasis of intestinal microbiota, increase the levels of short-chain fatty acids and their receptors, and suppress the loss of intestinal tight junction proteins. In addition, the results of plasma non-targeted metabolomics revealed that pterostilbene could modulate differential metabolites and metabolic pathways associated with inflammation, thereby suppressing systemic inflammation in DCI mice. Collectively, our study found for the first time that pterostilbene could alleviate diabetic cognitive dysfunction by inhibiting the TLR4/NF-κB pathway through the microbiota-gut-brain axis, which may be one of the potential mechanisms for its neuroprotective effects.PMID:37037513 | DOI:10.1002/ptr.7827

Bioresour Technol. 2023 Apr 8:129041. doi: 10.1016/j.biortech.2023.129041. Online ahead of print.ABSTRACTThe microalgae Haematococcus pluvialis is a commercial source of natural astaxanthin. However, mature cells develop rigid three-layer wall structures and a repulsive odor. This study applied a liquid static fermentation system to screen hydrolyzing microorganisms for cell wall hydrolysis. Baijiu jiuqu and Gutian hongqu were found to have promising potential for application. The fermentation using 2% baijiu jiuqu and 2% glucose for pre-activation achieved comparable recovery of carotenoids to homogenizer disruption methods and produced stable fragrance which may be attributed to ethyl octanoate, hexyl formate, and phenethyl butyrate, as revealed by gas chromatography-mass spectrometry analysis. The abundance of astaxanthin molecules was slightly affected by fermentation with fold change < 2, while molecules with higher fold change (>10) were mainly carbohydrates, lipids, and steroids proving the safety of the fermentation. This study provides a new scheme for the biorefining of Haematococcus. pluvialis, potentially contributing to the industrial production of natural astaxanthin.PMID:37037338 | DOI:10.1016/j.biortech.2023.129041

Clin Chim Acta. 2023 Apr 8:117330. doi: 10.1016/j.cca.2023.117330. Online ahead of print.ABSTRACTAIMS: To explore the maternal metabolic changes of fetal congenital heart disease (FCHD), and screen metabolic markers to establish a practical diagnostic model.METHODS: Maternal peripheral serum from 17 FCHD and 63 non-FCHD pregnant were analyzed by Ultra High-performance Liquid Chromatography-Mass/Mass (UPLC-MS/MS).RESULTS: In the FCHD and the non-FCHD, 132 metabolites were identified, including 35 differential metabolites enriched in the purine, caffeine, primary bile acid, and arachidonic acid metabolism pathway. Finally, the screened (+/-)9,10-dihydroxy-12Z-octadecenoic acid (AUC = 0.888) and 11,12-epoxy-(5Z,8Z,11Z)-icosatrienoic acid (AUC = 0.995) were incorporated into the logistic regression model. The AUC value of the two-metabolite model was 1.0, superior to proline (AUC = 0.867), uric acid (AUC = 0.789), glutamine (AUC = 0.705), and taurine (AUC = 0.923) previously reported. The clinical decision curve analysis (DCA) showed the highest clinical net benefit of the model, and internal validation by bootstrap shows the robustness of the model (Brier Score = 0.005).CONCLUSION: For the prenatal diagnosis of CHD, our findings are of great clinical significance. As an additional screening procedure, the identification model might be used to detect.PMID:37037297 | DOI:10.1016/j.cca.2023.117330

Environ Pollut. 2023 Apr 8:121584. doi: 10.1016/j.envpol.2023.121584. Online ahead of print.ABSTRACTMetal contamination is widespread, but only a few studies have evaluated the toxicological risks of metals (Cd, Cu, and Pb) in earthworms from farmlands in North China (Hebei province). Amynthas hupeiensis, the dominant species in the study area, was used to determine the responses and detoxification mechanisms of uncontaminated (CK), and low (LM)-, and high (HM)-metal-contaminated soils following 7-, 14-, and 28-days exposure. Metal toxicity in LM and HM soils inhibited the biomass of A. hupeiensis. The concentrations of Cd in A. hupeiensis bodies indicated accumulated Cd appeared to remain steady with prolonged exposure, while Cu/Pb increased significantly with soil levels. Bioaccumulation occurred in the order Cd > Pb > Cu in LM soil, and in the order Cd > Cu ≈ Pb in HM soil, which was attributed to differences in available fractions between LM and HM soils. Physiological levels of biomarkers in A. hupeiensis were determined, including total protein (TP), glutathione (GSH), glutathione peroxidase (GPx), acetylcholinesterase (AChE), and malondialdehyde (MDA). Deviations in GSH, GPx, and AChE were considered to denote sensitive biomarkers using the IBRv2 index. Metabolomics data (1H nuclear magnetic resonance-based) revealed changes in metabolites following 28-days exposure to LM and HM soils. Differences in metabolism in A. hupeiensis following exposure to LM and HM were related to energy metabolism, amino acid biosynthesis, glycerophospholipid metabolism, inositol phosphate metabolism, and glutathione metabolism. Metal stress from LM and HM soils disturbed osmoregulation, resulting in oxidative stress, destruction of cell membranes and inflammation, and altered levels of amino acids required for energy by A. hupeiensis. These findings provide biochemical insights into the physiological and metabolic mechanisms underlying the ability of A. hupeiensis to resist metal stress, and for assessing the environmental risks of metal-contaminated soils in farmland in North China.PMID:37037277 | DOI:10.1016/j.envpol.2023.121584

Kidney Blood Press Res. 2023 Apr 10. doi: 10.1159/000530209. Online ahead of print.ABSTRACTINTRODUCTION: The glomerular filtration rate (GFR) is crucial for chronic kidney disease (CKD) diagnosis and therapy. Various studies have sought to recognize ideal endogenous markers to improve the estimated GFR (eGFR) for clinical practice. To screen out potential novel metabolites related to GFR (mGFR) measurement in CKD patients from the Chinese population, we identified more biomarkers for improving GFR estimation.METHODS: Fifty-three CKD participants were recruited from the third affiliated hospital of Sun Yat-sen University in 2020. For each participant, mGFR was evaluated by utilizing the plasma clearance of iohexol and collecting serum samples for untargeted metabolomics analyses by Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy (UPLC-MS/MS). All participants were divided into four groups according to mGFR. The metabolite peak area data were uploaded to MetaboAnalyst5.0 for one-way ANOVA, principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) and confirmed the metabolites whose levels increased or decreased with mGFR and Variable Importance in Projection (VIP) values>1. Metabolites were ranked by correlation with the original values of mGFR, and metabolites with a correlation coefficient>0.8 and VIP >2 were identified.RESULTS: We screened out 198 metabolites that increased or decreased with mGFR decline. After ranking by correlation with mGFR, the top 50 metabolites were confirmed. Further studies confirmed the 10 most highly correlated metabolites.CONCLUSION: We screened out the metabolites that increased or decreased with mGFR decline in CKD patients from the Chinese population, and 10 of them were highly correlated. They are potential novel metabolites to improve GFR estimation.PMID:37037191 | DOI:10.1159/000530209

Proc Natl Acad Sci U S A. 2023 Apr 18;120(16):e2220134120. doi: 10.1073/pnas.2220134120. Epub 2023 Apr 10.ABSTRACTBromo- and extra-terminal domain inhibitors (BETi) have exhibited therapeutic activities in many cancers. However, the mechanisms controlling BETi response and resistance are not well understood. We conducted genome-wide loss-of-function CRISPR screens using BETi-treated KMT2A-rearranged (KMT2A-r) cell lines. We revealed that Speckle-type POZ protein (SPOP) gene (Speckle Type BTB/POZ Protein) deficiency caused significant BETi resistance, which was further validated in cell lines and xenograft models. Proteomics analysis and a kinase-vulnerability CRISPR screen indicated that cells treated with BETi are sensitive to GSK3 perturbation. Pharmaceutical inhibition of GSK3 reversed the BETi-resistance phenotype. Based on this observation, a combination therapy regimen inhibiting both BET and GSK3 was developed to impede KMT2A-r leukemia progression in patient-derived xenografts in vivo. Our results revealed molecular mechanisms underlying BETi resistance and a promising combination treatment regimen of ABBV-744 and CHIR-98014 by utilizing unique ex vivo and in vivo KMT2A-r PDX models.PMID:37036970 | DOI:10.1073/pnas.2220134120

Planta. 2023 Apr 10;257(5):95. doi: 10.1007/s00425-023-04129-9.ABSTRACTThe keys to alkali-stress resistance of barren-tolerant wild soybean lay in enhanced reutilization of reserves in cotyledons as well as improved antioxidant protection and organic acid accumulation in young roots. Soil alkalization of farmlands is increasingly serious, adversely restricting crop growth and endangering food security. Here, based on integrated analysis of transcriptomics and metabolomics, we systematically investigated changes in cotyledon weight and young root growth in response to alkali stress in two ecotypes of wild soybean after germination to reveal alkali-resistance mechanisms in barren-tolerant wild soybean. Compared with barren-tolerant wild soybean, the dry weight of common wild soybean cotyledons under alkali stress decreased slowly and the length of young roots shortened. In barren-tolerant wild soybean, nitrogen-transport amino acids asparagine and glutamate decreased in cotyledons but increased in young roots, and nitrogen-compound transporter genes and genes involved in asparagine metabolism were significantly up-regulated in both cotyledons and young roots. Moreover, isocitric, succinic, and L-malic acids involved in the glyoxylate cycle significantly accumulated and the malate synthetase gene was up-regulated in barren-tolerant wild soybean cotyledons. In barren-tolerant wild soybean young roots, glutamate and glycine related to glutathione metabolism increased significantly and the glutathione reductase gene was up-regulated. Pyruvic acid and citric acid involved in pyruvate-citrate metabolism increased distinctly and genes encoding pyruvate decarboxylase and citrate synthetase were up-regulated. Integrated analysis showed that the keys to alkali-stress resistance of barren-tolerant wild soybean lay in enhanced protein decomposition, amino acid transport, and lipolysis in cotyledons as well as improved antioxidant protection and organic acid accumulation in young roots. This study provides new ideas for the exploitation and utilization of wild soybean resources.PMID:37036535 | DOI:10.1007/s00425-023-04129-9

Microbiol Spectr. 2023 Apr 10:e0206722. doi: 10.1128/spectrum.02067-22. Online ahead of print.ABSTRACTHepatectomy is a common clinical procedure for the treatment of many liver diseases, and the successful recovery of a patient's liver metabolism and function after surgery is crucial for a good prognosis. The objective of this study was to elucidate the metabolic response to hepatectomy using high-throughput sequencing analysis of 16S rRNA gene, metabolomics, and proteomics data. Fecal and serum samples from beagle dogs were collected on day 0 (LH0), day 7 (LH7), and day 28 (LH28) after laparoscopic partial hepatectomy. Liver tissue samples were taken on LH0 and LH7. Dysbiosis in the fecal microbiota was explored, and host-microbiome interactions based on global metabolic and protein profiles and inflammatory processes were determined. Results showed that the relative abundance of Allobaculum and Turicibacter was decreased and that of Escherichia-Shigella was increased after hepatectomy (P < 0.05); the phenylalanine, tyrosine, and tryptophan biosynthetic pathway, along with the phenylalanine and aminoacyl-tRNA biosynthetic pathway, was significantly associated with liver injury. The serum metabolites l-phenylalanine and l-arginine were useful as biomarkers, and the fecal metabolite l-threonine was a signature target monitor for liver recovery. The proteomics profile revealed 412 significantly different proteins and further highlighted two key signaling pathways (mitogen-activated protein kinase [MAPK] and peroxisome proliferator-activated receptor [PPAR]) involved in the response to liver injury. We systematically explored the metabolic mechanism of liver injury and recovery, providing new insights into effective ways to promote recovery after hepatectomy and improve liver function and long-term survival. These fundamental studies on hepatectomy will provide the basis for future advances in treatment and recovery from common liver diseases. IMPORTANCE As the largest parenchymal organ, the liver is a target for bacterial and viral infections, nonalcoholic fatty liver disease (NAFLD), cirrhosis, cancer, and many other diseases, constituting a serious worldwide problem. The treatment for many of these diseases involves hepatectomy. Here, we show that aberrant inflammatory processes after hepatectomy of the liver as reflected in the association between liver metabolism and gut microbiota create a grave risk. This study investigated the mechanisms of gut microbiota and host metabolism involved in liver injury and recovery after hepatectomy, using proteomics to reveal the mechanisms of postoperative liver injury and a comprehensive multi-omics approach to identify changes in metabolism after hepatectomy.PMID:37036349 | DOI:10.1128/spectrum.02067-22

Curr Protoc. 2023 Apr;3(4):e720. doi: 10.1002/cpz1.720.ABSTRACTWith the rapid increase in clinical exome and genome sequencing, the number of variants of uncertain significance (VUS) that are reported continues to rise, which poses a significant barrier to interpretation of genetic findings. For metabolic disorders, biochemical testing can help alleviate this burden of variant interpretation by providing functional validation of uncertain genetic findings in many cases. However, a major limitation of traditional biochemical testing is the targeted, narrow range of analytes clinically available, resulting in delays in diagnosis if testing is negative. Untargeted metabolomic screening offers higher diagnostic yield and assays for thousands of metabolites across multiple metabolic pathways in a single test, saving time and resources for patients, families, and physicians. When integrated with exome or genome sequencing, untargeted metabolomic screening improves diagnostic outcomes by providing functional validation of genetic findings, particularly for VUS. Here, we present representative cases across the breadth of metabolic pathways as examples of the utility of metabolomics in genomic variant classification. © 2023 Wiley Periodicals LLC.PMID:37036266 | DOI:10.1002/cpz1.720

J Vis Exp. 2023 Mar 24;(193). doi: 10.3791/65029.ABSTRACTHuman industries generate hundreds of thousands of chemicals, many of which have not been adequately studied for environmental safety or effects on human health. This deficit of chemical safety information is exacerbated by current testing methods in mammals that are expensive, labor-intensive, and time-consuming. Recently, scientists and regulators have been working to develop new approach methodologies (NAMs) for chemical safety testing that are cheaper, more rapid, and reduce animal suffering. One of the key NAMs to emerge is the use of invertebrate organisms as replacements for mammalian models to elucidate conserved chemical modes of action across distantly related species, including humans. To advance these efforts, here, we describe a method that uses the fruit fly, Drosophila melanogaster, to assess chemical safety. The protocol describes a simple, rapid, and inexpensive procedure to measure the viability and feeding behavior of exposed adult flies. In addition, the protocol can be easily adapted to generate samples for genomic and metabolomic approaches. Overall, the protocol represents an important step forward in establishing Drosophila as a standard model for use in precision toxicology.PMID:37036230 | DOI:10.3791/65029

Bioact Mater. 2023 Mar 28;26:452-464. doi: 10.1016/j.bioactmat.2023.03.012. eCollection 2023 Aug.ABSTRACTDeveloping functional ductal organoids (FDOs) is essential for liver regenerative medicine. We aimed to construct FDOs with biliary tree networks in rat decellularized liver scaffolds (DLSs) with primary cholangiocytes isolated from mouse bile ducts. The developed FDOs were dynamically characterized by functional assays and metabolomics for bioprocess clarification. FDOs were reconstructed in DLSs retaining native structure and bioactive factors with mouse primary cholangiocytes expressing enriched biomarkers. Morphological assessment showed that biliary tree-like structures gradually formed from day 3 to day 14. The cholangiocytes in FDOs maintained high viability and expressed 11 specific biomarkers. Basal-apical polarity was observed at day 14 with immunostaining for E-cadherin and acetylated α-tubulin. The rhodamine 123 transport assay and active collection of cholyl-lysyl-fluorescein exhibited the specific functions of bile secretion and transportation at day 14 compared to those in monolayer and hydrogel culture systems. The metabolomics analysis with 1075 peak pairs showed that serotonin, as a key molecule of the tryptophan metabolism pathway linked to biliary tree reconstruction, was specifically expressed in FDOs during the whole period of culture. Such FDOs with biliary tree networks and serotonin expression may be applied for disease modeling and drug screening, which paves the way for future clinical therapeutic applications.PMID:37035760 | PMC:PMC10073412 | DOI:10.1016/j.bioactmat.2023.03.012

World J Diabetes. 2023 Mar 15;14(3):255-270. doi: 10.4239/wjd.v14.i3.255.ABSTRACTBACKGROUND: In recent years, the incidence of type 2 diabetes (T2DM) has shown a rapid growth trend. Goto Kakizaki (GK) rats are a valuable model for the study of T2DM and share common glucose metabolism features with human T2DM patients. A series of studies have indicated that T2DM is associated with the gut microbiota composition and gut metabolites. We aimed to systematically characterize the faecal gut microbes and metabolites of GK rats and analyse the relationship between glucose and insulin resistance.AIM: To evaluate the gut microbial and metabolite alterations in GK rat faeces based on metagenomics and untargeted metabolomics.METHODS: Ten GK rats (model group) and Wistar rats (control group) were observed for 10 wk, and various glucose-related indexes, mainly including weight, fasting blood glucose (FBG) and insulin levels, homeostasis model assessment of insulin resistance (HOMA-IR) and homeostasis model assessment of β cell (HOMA-β) were assessed. The faecal gut microbiota was sequenced by metagenomics, and faecal metabolites were analysed by untargeted metabolomics. Multiple metabolic pathways were evaluated based on the differential metabolites identified, and the correlations between blood glucose and the gut microbiota and metabolites were analysed.RESULTS: The model group displayed significant differences in weight, FBG and insulin levels, HOMA-IR and HOMA-β indexes (P < 0.05, P < 0.01) and a shift in the gut microbiota structure compared with the control group. The results demonstrated significantly decreased abundances of Prevotella sp. CAG:604 and Lactobacillus murinus (P < 0.05) and a significantly increased abundance of Allobaculum stercoricanis (P < 0.01) in the model group. A correlation analysis indicated that FBG and HOMA-IR were positively correlated with Allobaculum stercoricanis and negatively correlated with Lactobacillus murinus. An orthogonal partial least squares discriminant analysis suggested that the faecal metabolic profiles differed between the model and control groups. Fourteen potential metabolic biomarkers, including glycochenodeoxycholic acid, uric acid, 13(S)-hydroxyoctadecadienoic acid (HODE), N-acetylaspartate, β-sitostenone, sphinganine, 4-pyridoxic acid, and linoleic acid, were identified. Moreover, FBG and HOMA-IR were found to be positively correlated with glutathione, 13(S)-HODE, uric acid, 4-pyridoxic acid and allantoic acid and ne-gatively correlated with 3-α, 7-α, chenodeoxycholic acid glycine conjugate and 26-trihydroxy-5-β-cholestane (P < 0.05, P < 0.01). Allobaculum stercoricanis was positively correlated with linoleic acid and sphinganine (P < 0.01), and 2-methyl-3-hydroxy-5-formylpyridine-4-carboxylate was negatively associated with Prevotella sp. CAG:604 (P < 0.01). The metabolic pathways showing the largest differences were arginine biosynthesis; primary bile acid biosynthesis; purine metabolism; linoleic acid metabolism; alanine, aspartate and glutamate metabolism; and nitrogen metabolism.CONCLUSION: Metagenomics and untargeted metabolomics indicated that disordered compositions of gut microbes and metabolites may be common defects in GK rats.PMID:37035219 | PMC:PMC10075032 | DOI:10.4239/wjd.v14.i3.255

Front Plant Sci. 2023 Mar 24;14:1155258. doi: 10.3389/fpls.2023.1155258. eCollection 2023.ABSTRACTPlants have evolved circadian clock systems that enable biological processes to occur in tandem with periodic changes in the environment. However, it is largely unknown whether crosstalk occurs between the circadian clock and the response to herbicide in rice. We identified 19 conserved rhythmic metabolites which were response to pesticide application and their metabolic abundance peaked mainly at ZT2 or ZT14-ZT18. We found a series of glyphosate, s-Metolachlor, fenclorim, metcamifen and GA3 response genes were expressed following stable circadian rhythms. In order to determine the patterns of their temporal expression, co-expression network analysis was done on 10,467 genes that were periodically expressed throughout a 24-hour period. Next, we identified 4,031 potential direct target genes of OsCCA1 in using DAP-seq data for OsCCA1. Of these, 339, 22, 53, 53 and 63 genes showed a response to glyphosate, s-Metolachlor, fenclorim, metcamifen and GA3 application, respectively. And they were mainly phased from dusk to midnight. Interestingly, we identified significant OsCCA1 binding peaks in the promoter regions of four herbicide resistance genes, including OsCYP81A12, OsCYP81E22, OsCYP76C2, and OsCYP76C4. Finally, we found that herbicide application could affects the expression of some of the central oscillator genes of the rice circadian clock. Here, we used multi-omics data to reveal the crosstalk between the circadian clock and herbicide response processes at the epigenomics, transcriptome, and metabolome levels in rice. This work will serve as a theoretical guide for identifying rhythmic herbicide targets, leading to the creation of new herbicides or the breeding of crops resistant to herbicides.PMID:37035069 | PMC:PMC10080033 | DOI:10.3389/fpls.2023.1155258