Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

Chemometric-guided chemical marker selection: A case study of the heat-clearing herb <em>Scrophularia ningpoensis</em>

Fri, 14/04/2023 - 12:00
Front Plant Sci. 2023 Mar 17;14:1153710. doi: 10.3389/fpls.2023.1153710. eCollection 2023.ABSTRACTThe selection of medicinal plants' chemical markers focuses on bioactivity as the primary goal, followed by the nature of secondary metabolites, their stability, and availability. However, herbal medicines are valued for their complex and holistic pharmacological effects. A correct chemical marker can be carefully selected by a systematic clarification of their chemical-biological relationships. In the current study, the multi-informative molecular networking (MIMN) approach was employed to construct the anti-inflammatory metabolomic pattern of a heat-clearing herb, Scrophularia ningpoensis Hemsl. (S. ningpoensis). The MIMN molecular families characterized by cinnamic acid glycosides showed a higher bioactivity score compared with the other two major chemical classes (iridoid glycosides and iridoid-cinnamic acid glycosides). The Global Natural Product Social Molecular Networking (GNPS) and Reaxys database were used to assist in the putative annotation of eighteen metabolites from the bioactive and non-bioactive molecular families. The anti-inflammatory validation step was based on the detection of reactive oxygen species (ROS) generation by activated human neutrophils. All compounds from the bioactive MIMN molecular families dose-dependently inhibited the total ROS generation promoted by fMLF (IC50: 0.04-0.42 μM), while the compounds from non-bioactive MIMN clusters did not show any significant anti-inflammatory effect. The ROS-dependent anti-inflammatory activity of these cinnamic acid glycosides was attributed to their oxygen radical scavenging ability. The most abundant cinnamic acid glycoside, angoroside C (IC50: 0.34 μM) was suggested to be selected as a chemical marker for S. ningpoensis. In this study, the MIMN platform was applied to assist in the chemical marker selection of S. ningpoensis. The correct selection of markers will aid in the compilation and revision of herbal monographs and pharmacopeias resulting in the precise analysis and classification of medicinal plants on a scientific basis.PMID:37056509 | PMC:PMC10088908 | DOI:10.3389/fpls.2023.1153710

Overexpression of the aldehyde dehydrogenase <em>AhALDH3H1</em> from <em>Arachis hypogaea</em> in soybean increases saline-alkali stress tolerance

Fri, 14/04/2023 - 12:00
Front Plant Sci. 2023 Mar 28;14:1165384. doi: 10.3389/fpls.2023.1165384. eCollection 2023.ABSTRACTSoybean production is severely hampered by saline-alkaline stress caused by saline-alkalization. Plants have aldehydrogenase (ALDH) family members that convert reactive aldehydes to carboxylic acids to remove active aldehyde molecules. However, little is known about the increased saline-alkali tolerance caused by the ALDH function in soybean. Here, we introduced a previously identified ALDH coding gene AhALDH3H1 from Arachis hypogaea into the soybean genome to investigate its critical role in response to saline-alkali stress. Transgenic soybean with increased aldehyde dehydrogenase activity showed significant tolerance to saline-alkali stress. It reduced malondialdehyde (MDA) content compared to its receptor, suggesting that over-expression of AhALDH3H1 accelerated soybean tolerance to saline-alkali stress by increasing aldehyde dehydrogenase activity, which is responsible for scavenging toxic MDA. To further analyze the inner mechanisms that allow transgenic plants to tolerate saline-alkali stress, we sequenced the transcriptome and metabolome of P3 (wild type, WT) and transgenic lines which were separately treated with water and a saline-alkali solution. When subjected to saline-alkali stress, the integrated analysis of the transcriptome and metabolome suggested that several genes related to cell wall structure crucial for preserving cell wall extensibility and plasticity were largely responsible for restoring homeostasis within the transgenic cells compared to WT. Metabolites, including both necessary ingredients for cell wall genesis and harmful production produced during the saline-alkali stress response, could be transported efficiently with the help of the ABC transporter, reducing the negative effects of saline-alkali stress. These findings suggest that introducing AhALDH3H1 increases transgenic soybean tolerance to saline-alkali stress may through cell wall structure maintenance and metabolites transport.PMID:37056489 | PMC:PMC10086354 | DOI:10.3389/fpls.2023.1165384

Dihydroartemisinin Potentiates VEGFR-TKIs Antitumorigenic Effect on Osteosarcoma by Regulating Loxl2/VEGFA Expression and Lipid Metabolism Pathway

Fri, 14/04/2023 - 12:00
J Cancer. 2023 Mar 27;14(5):809-820. doi: 10.7150/jca.81623. eCollection 2023.ABSTRACTAnti-angiogenesis therapy has shown significant anti-tumor effects against a variety of cancers. But resistance to antiangiogenic drugs, intrinsic and evasive, is frequently found in patients during treatment. Here, we report that dihydroartemisinin (DHA), a derivative of the Chinese medicine artemisinin, enhances antiangiogenic drug-induced cytotoxicity in osteosarcoma (OS) cells. Proteomics analysis revealed that DHA treatment significantly affected the activity of the collagen-modifying enzyme lysyl oxidase-like 2 (LOXL2), a regulatory gene associated with poor prognosis of OS. Furthermore, we found that DHA reduced the expression of vascular endothelial growth factor (VEGFA) by downregulating LOXL2. This mechanism was confirmed by QRT-PCR, western blot, and ELISA assays. Correspondingly, vector-enforced expression of LOXL2 markedly reduced VEGFA secretion. Untargeted metabolomic analysis revealed that the lipid metabolism that confers antiangiogenic drug resistance, was also interfered with by DHA. Thus, DHA not only exerts antitumor effects in OS cells directly but also synergizes with the antiangiogenic drug by regulating vascular endothelial growth factor A (VEGFA) expression and lipid metabolism.PMID:37056396 | PMC:PMC10088882 | DOI:10.7150/jca.81623

Erratum: Glutathione levels are associated with methotrexate resistance in acute lymphoblastic leukemia cell lines

Fri, 14/04/2023 - 12:00
Front Oncol. 2023 Mar 28;13:1190120. doi: 10.3389/fonc.2023.1190120. eCollection 2023.ABSTRACT[This corrects the article DOI: 10.3389/fonc.2022.1032336.].PMID:37056334 | PMC:PMC10086418 | DOI:10.3389/fonc.2023.1190120

Assessing the causal relationships between human blood metabolites and the risk of NAFLD: A comprehensive mendelian randomization study

Fri, 14/04/2023 - 12:00
Front Genet. 2023 Mar 28;14:1108086. doi: 10.3389/fgene.2023.1108086. eCollection 2023.ABSTRACTBackground: Non-alcoholic fatty liver disease (NAFLD) is a liver disease associated with obesity, insulin resistance, type 2 diabetes mellitus (T2DM), and metabolic syndrome. The risk factors for NAFLD have not been identified. Metabolic dysfunction has been found to be an important factor in the pathogenesis and progression of NAFLD. However, the causal impact of blood metabolites on NAFLD is unclear. Methods: We performed a two-sample Mendelian randomization (MR) study. A genome-wide association study (GWAS) with 7824 participants provided data on 486 human blood metabolites. Outcome information was obtained from a large-scale GWAS meta-analysis of NAFLD, which contained 8,434 cases and 770,180 controls of Europeans. The inverse variance weighted (IVW) model was chosen as the primary two-sample MR analysis approach, followed by sensitivity analyses such as the heterogeneity test, horizontal pleiotropy test, and leave-one-out analysis. In addition, we performed replication, meta-analysis, and metabolic pathway analysis. We further conducted colocalization analysis to deeply reflect the causality. Results: After rigorous genetic variant selection, IVW, sensitivity analysis, replication, and meta-analysis, two known metabolites were identified as being associated with the development of NAFLD [biliverdin: OR = 1.45; 95% CI 1.20-1.75; p = 0.0001; myristoleate: OR = 0.57; 95% CI 0.39-0.83; p = 0.0030]. Conclusion: By combining genomics with metabolomics, our findings provide a new perspective on the underlying mechanisms of NAFLD and have important implications for the screening and prevention of NAFLD.PMID:37056283 | PMC:PMC10086196 | DOI:10.3389/fgene.2023.1108086

Stable isotope labeling-mass spectrometry as a new approach to determine remyelination

Fri, 14/04/2023 - 12:00
Neural Regen Res. 2023 Oct;18(10):2184-2185. doi: 10.4103/1673-5374.369104.NO ABSTRACTPMID:37056128 | DOI:10.4103/1673-5374.369104

Bacillus coagulans XY2 ameliorates copper-induced toxicity by bioadsorption, gut microbiota and lipid metabolism regulation

Fri, 14/04/2023 - 12:00
J Hazard Mater. 2023 Mar 5;445:130585. doi: 10.1016/j.jhazmat.2022.130585. Epub 2022 Dec 9.ABSTRACTExcessive copper pollutes the environment and endangers human health, attracting plenty of global attention. In this study, a novel strain named Bacillus coagulans XY2 was discovered to have a great copper tolerance and adsorption capacity. B. coagulans XY2 might maintain copper homeostasis through multisystem synergies of copper resistance, sulfur metabolism, Fe-S cluster assembly, and siderophore transport. In mice, by promoting the expression of SREBF-1 and SREBF-2 and their downstream genes, B. coagulans XY2 significantly inhibited the copper-induced decrease in weight growth rate, ameliorated dyslipidemia, restored total cholesterol and triglyceride contents both in serum and liver. Furthermore, B. coagulans XY2 recovered the diversity of gut microbiota and suppressed the copper-induced reduction in the ratio of Firmicutes to Bacteroidota. Serum metabolomics analysis showed that the alleviating effect of B. coagulans XY2 on copper toxicity was mainly related to lipid metabolism. For the first time, we demonstrated mechanisms of copper toxicity mitigation by B. coagulans XY2, which was related to self-adsorption, host copper excretion promotion, and lipid metabolism regulation. Moreover, working model of B. coagulans XY2 on copper homeostasis was predicted by whole-genome analysis. Our study provides a new solution for harmfulness caused by copper both in human health and the environment.PMID:37055990 | DOI:10.1016/j.jhazmat.2022.130585

Determination of the Time since Deposition of Blood-traces in a Forensic Context: Application of Untargeted LC-HR-MS/MS Metabolomics Profiling

Fri, 14/04/2023 - 12:00
Drug Test Anal. 2023 Apr 13. doi: 10.1002/dta.3480. Online ahead of print.ABSTRACTBeing able to attest when a bloodstain was deposited at a crime scene can be invaluable to a prosecution process, and methods to provide that information have long been desired. Determining the Time since Deposition (TsD) of a trace would allow placing a subject both in space and time to the crime scene - or prove that a trace left by that person was unrelated to it, because it was deposited before or after the time a crime had occurred. To this day, no method for TsD-determination has made its way into routine forensic casework, mainly because of the numerous challenges that await when trying to understand and account for all the influencing and confounding factors that affect the aging process (such as, e.g., temperature, UV-light exposure, or humidity). Here, we present an untargeted metabolomics-based study using liquid-chromatography high-resolution mass-spectrometry (LC-HRMS) and data-dependent acquisition to analyze blood samples aged under two distinctly different storage conditions over 48 weeks. Global differences in age- and storage-dependent changes in blood metabolomes were described, and TsD-classification strategies based on qualitative and quantitative assessment of molecular features (MFs) have been proposed. Based on the selected criteria to best predict the TsD, the dipeptide Phenylalanylalanine (PheAla) can be considered as a promising candidate for TsD prediction. In essence, changes in the blood metabolome dynamics showed a strong association with increasing TsD, but significant differences depending on storage conditioning were observed, facilitating the need to study further the influence of (individual) influencing factors on TsD-determination.PMID:37055932 | DOI:10.1002/dta.3480

Lipidomics and Metabolomics in Infant Atopic Dermatitis: What's the Correlation with Early Nutrition?

Fri, 14/04/2023 - 12:00
Curr Pediatr Rev. 2023 Apr 11. doi: 10.2174/1573396320666230411093122. Online ahead of print.ABSTRACTTo date, the complex picture of atopic dermatitis (AD) has not yet been fully clarified, despite the important prevalence of this disease in the pediatric population (20%) and the possibility of persistence into adulthood, with important implications for the quality of life of those affected, as well as significant social and financial costs. The most recent scientific evidence suggests a new interpretation of AD, highlighting the important role of the environment, particularly that of nutrition in the early stages of development. In fact, the new indications seem to point out the harmful effect of elimination diets, except in rare cases, the uselessness of chrono-insertions during complementary feeding and some benefits, albeit weak, of breastfeeding in those at greater risk. In this context, metabolomics and lipidomics can be necessary for a more in-depth knowledge of the complex metabolic network underlying this pathology. In fact, an alteration of the metabolic contents in children with AD has been highlighted, especially in correlation to the intestinal microbiota. While preliminary lipidomic studies showed the usefulness of a more in-depth knowledge of the alterations of the skin barrier to improve the development of baby skin care products. Therefore, investigating the response of different allergic phenotypes could be useful for better patient management and understanding, thus providing an early intervention on dysbiosis necessary to regulate the immune response from the earliest stages of development.PMID:37055903 | DOI:10.2174/1573396320666230411093122

Metabolomic and Proteomic Identification of Serum Exosome for Hypoxic Preconditioning Participants

Thu, 13/04/2023 - 12:00
Oxid Med Cell Longev. 2023 Apr 13;2023:5509913. doi: 10.1155/2023/5509913. eCollection 2023.ABSTRACTBACKGROUND: In high-altitude areas, hypoxic stress can elicit a series of physiological responses in humans. Exosomes play important roles in both local and distal cellular communications.METHODS: We used ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) studies to analyze the differentially expressed metabolomics and proteomics in serum exosome of hypoxic preconditioning participants and control subjects in the hypoxic conditions.RESULTS: Fifty-seven military personnel were divided into hypoxic preconditioning group (n = 27) and control group (n = 30). One hundred thirty-six differentially expressed serum exosomal metabolites were found between the hypoxic preconditioning and control groups in the hypoxic conditions, and these differentially expressed metabolites were enriched in pathways related to lysine degradation, butanoate metabolism, GABAergic synapse, histidine metabolism, and linoleic acid metabolism. In addition, hypoxic preconditioning participants showed 102 excellent differential expressions of proteomics compared to controls, which involved actin cytoskeleton organization, hemostasis, complement and coagulation cascades, vesicle-medicated transport, wound healing, etc.CONCLUSIONS: We revealed that the expression of exosomal metabolites and proteomics in hypoxic preconditioning participants was significantly different compared to controls in hypoxic conditions.PMID:37089582 | PMC:PMC10118903 | DOI:10.1155/2023/5509913

Untargeted <sup>1</sup>H NMR-based metabolomics and multi-technique data fusion: A promising combined approach for geographical and processing authentication of thyme by multivariate statistical analysis

Thu, 13/04/2023 - 12:00
Food Chem. 2023 Apr 13;420:136156. doi: 10.1016/j.foodchem.2023.136156. Online ahead of print.ABSTRACTThyme is a culinary herb highly susceptible to increasing mislabeling occurring in the spice industry. In this study, proton nuclear magnetic resonance spectroscopy (1H NMR) combined with multivariate statistics was successfully applied with two authenticity purposes: (1) tracing thyme metabolic differences among three relevant geographical regions (Morocco, Spain, and Poland), and (2) assessing the influence of sterilization processing on the metabolic fingerprint. Multivariate data analysis provided six and seven key geographical and processing markers, respectively, including thymol, organic acids, chlorogenic acid, and some carbohydrates (e.g., sucrose). Additionally, for the first time, a mid-level data fusion approach was tested for thyme authenticity combining three complementary and synergic analytical platforms: gas and liquid chromatography coupled with high-resolution mass spectrometry, and 1H NMR spectroscopy, providing a comprehensive metabolomics insight into the origin and processing effects on thyme fingerprinting, and opening the path to new metabolomics approaches for quality control in the spice industry.PMID:37075575 | DOI:10.1016/j.foodchem.2023.136156

Divergence of Liver Lipidomes in Tibetan and Yorkshire Pigs Living at Different Altitudes

Thu, 13/04/2023 - 12:00
Molecules. 2023 Mar 27;28(7):2991. doi: 10.3390/molecules28072991.ABSTRACTThe Tibetan pig is a characteristic breed of the Qinghai-Tibet Plateau with distinct physiological and meat quality attributes. The liver lipid profile can offer an important perspective to explore the uniqueness of Tibetan pigs. A quantitative comparison of liver lipidomes revealed significant differences in the lipid profiles between Tibetan and Yorkshire pigs raised at different altitudes. The abundance of lipids in the livers of pigs raised at a high altitude was higher than that of pigs raised at a lower altitude, whereas the abundance of lipids in the livers of Yorkshire pigs was higher than that of Tibetan pigs raised at the same altitude. Of the 1101 lipids identified, 323 and 193 differentially abundant lipids (DALs) were identified in the pairwise comparisons of Tibetan and Yorkshire pigs raised at different altitudes, respectively. The DALs of Tibetan pigs consisted mainly of 161 triglycerides, along with several acylcarnitines, represented by carnitine C2:0, and significant changes in the abundance of some phospholipids. The DALs of Yorkshire pigs were more complex, with significant increases in the abundance of triglycerides, cholesteryl esters, and free fatty acids, and decreases in the abundance of some phospholipids. This research provides strong theoretical and data support for the high-quality development of the highland livestock industry.PMID:37049754 | DOI:10.3390/molecules28072991

BUDDY: molecular formula discovery via bottom-up MS/MS interrogation

Thu, 13/04/2023 - 12:00
Nat Methods. 2023 Apr 13. doi: 10.1038/s41592-023-01850-x. Online ahead of print.ABSTRACTA substantial fraction of metabolic features remains undetermined in mass spectrometry (MS)-based metabolomics, and molecular formula annotation is the starting point for unraveling their chemical identities. Here we present bottom-up tandem MS (MS/MS) interrogation, a method for de novo formula annotation. Our approach prioritizes MS/MS-explainable formula candidates, implements machine-learned ranking and offers false discovery rate estimation. Compared with the mathematically exhaustive formula enumeration, our approach shrinks the formula candidate space by 42.8% on average. Method benchmarking on annotation accuracy was systematically carried out on reference MS/MS libraries and real metabolomics datasets. Applied on 155,321 recurrent unidentified spectra, our approach confidently annotated >5,000 novel molecular formulae absent from chemical databases. Beyond the level of individual metabolic features, we combined bottom-up MS/MS interrogation with global optimization to refine formula annotations while revealing peak interrelationships. This approach allowed the systematic annotation of 37 fatty acid amide molecules in human fecal data. All bioinformatics pipelines are available in a standalone software, BUDDY ( https://github.com/HuanLab/BUDDY ).PMID:37055660 | DOI:10.1038/s41592-023-01850-x

Fetal lung hypoxia and energetic cell failure in the nitrofen-induced congenital diaphragmatic hernia rat model

Thu, 13/04/2023 - 12:00
Pediatr Surg Int. 2023 Apr 13;39(1):180. doi: 10.1007/s00383-023-05452-8.ABSTRACTPURPOSE: Congenital diaphragmatic hernia (CDH) pathogenesis is poorly understood. We hypothesize that fetal CDH lungs are chronically hypoxic because of lung hypoplasia and tissue compression, affecting the cell bioenergetics as a possible explanation for abnormal lung development.METHODS: To investigate this theory, we conducted a study using the rat nitrofen model of CDH. We evaluated the bioenergetics status using H1 Nuclear magnetic resonance and studied the expression of enzymes involved in energy production, the hypoxia-inducible factor 1α, and the glucose transporter 1.RESULTS: The nitrofen-exposed lungs have increased levels of hypoxia-inducible factor 1α and the main fetal glucose transporter, more evident in the CDH lungs. We also found imbalanced AMP:ATP and ADP:ATP ratios, and a depleted energy cellular charge. Subsequent transcription levels and protein expression of the enzymes involved in bioenergetics confirm the attempt to prevent the energy collapse with the increase in lactate dehydrogenase C, pyruvate dehydrogenase kinase 1 and 2, adenosine monophosphate deaminase, AMP-activated protein kinase, calcium/calmodulin-dependent protein kinase 2, and liver kinase B1, while decreasing ATP synthase.CONCLUSION: Our study suggests that changes in energy production could play a role in CDH pathogenesis. If confirmed in other animal models and humans, this could lead to the development of novel therapies targeting the mitochondria to improve outcomes.PMID:37055635 | DOI:10.1007/s00383-023-05452-8

Longitudinal lipidomic signatures of all-cause and CVD mortality in American Indians: findings from the Strong Heart Study

Thu, 13/04/2023 - 12:00
Geroscience. 2023 Apr 13. doi: 10.1007/s11357-023-00793-7. Online ahead of print.ABSTRACTDyslipidemia is an independent and modifiable risk factor for aging and age-related disorders. Routine lipid panel cannot capture all individual lipid species in blood (i.e., blood lipidome). To date, a comprehensive assessment of the blood lipidome associated with mortality is lacking in large-scale community-dwelling individuals, especially in a longitudinal setting. Using liquid chromatograph-mass spectrometry, we repeatedly measured individual lipid species in 3,821 plasma samples collected at two visits (~ 5.5 years apart) from 1,930 unique American Indians in the Strong Heart Family Study. We first identified baseline lipids associated with risks for all-cause mortality and CVD mortality (mean follow-up period: 17.8 years) in American Indians, followed by replication of top hits in European Caucasians in the Malmö Diet and Cancer-Cardiovascular Cohort (n = 3,943, mean follow-up period: 23.7 years). The model adjusted age, sex, BMI, smoking, hypertension, diabetes, and LDL-c at baseline. We then examined the associations between changes in lipid species and risk of mortality. Multiple testing was controlled by false discovery rate (FDR). We found that baseline levels and longitudinal changes of multiple lipid species, e.g., cholesterol esters, glycerophospholipids, sphingomyelins, and triacylglycerols, were significantly associated with risks of all-cause or CVD mortality. Many lipids identified in American Indians could be replicated in European Caucasians. Network analysis identified differential lipid networks associated with risk of mortality. Our findings provide novel insight into the role of dyslipidemia in disease mortality and offer potential biomarkers for early prediction and risk reduction in American Indians and other ethnic groups.PMID:37055600 | DOI:10.1007/s11357-023-00793-7

Metabolomics analysis reveals metabolite changes during freeze-drying and oven-drying of Angelica dahurica

Thu, 13/04/2023 - 12:00
Sci Rep. 2023 Apr 13;13(1):6022. doi: 10.1038/s41598-023-32402-0.ABSTRACTAngelica dahurica (Angelica dahurica Fisch. ex Hoffm.) is widely used as a traditional Chinese medicine and the secondary metabolites have significant pharmacological activities. Drying has been shown to be a key factor affecting the coumarin content of Angelica dahurica. However, the underlying mechanism of metabolism is unclear. This study sought to determine the key differential metabolites and metabolic pathways related to this phenomenon. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based targeted metabolomics analysis was performed on Angelica dahurica that were freeze-drying (- 80 °C/9 h) and oven-drying (60 °C/10 h). Furthermore, the common metabolic pathways of paired comparison groups were performed based on KEEG enrichment analysis. The results showed that 193 metabolites were identified as key differential metabolites, most of which were upregulated under oven drying. It also displayed that many significant contents of PAL pathways were changed. This study revealed the large-scale recombination events of metabolites in Angelica dahurica. First, we identified additional active secondary metabolites apart from coumarins, and volatile oil were significantly accumulated in Angelica dahurica. We further explored the specific metabolite changes and mechanism of the phenomenon of coumarin upregulation caused by temperature rise. These results provide a theoretical reference for future research on the composition and processing method of Angelica dahurica.PMID:37055447 | DOI:10.1038/s41598-023-32402-0

Metabolomic Profiling and Drug Interaction Characterization Reveal Riboflavin as a Breast Cancer Resistance Protein -Specific Endogenous Biomarker that Demonstrates Prediction of Transporter Activity In Vivo

Thu, 13/04/2023 - 12:00
Drug Metab Dispos. 2023 Apr 13:DMD-AR-2023-001284. doi: 10.1124/dmd.123.001284. Online ahead of print.ABSTRACTAdvancement of endogenous biomarkers for drug transporters as a tool for assessing drug-drug interactions (DDIs) depends on initial identification of biomarker candidates and relies heavily on biomarker validation and its response to reference inhibitors in vivo. To identify endogenous biomarkers of breast cancer resistance protein (BCRP), we applied metabolomic approaches to profile plasma from Bcrp-/-, Mdr1a/1b-/-, and Bcrp/Mdr1a/1b-/- mice. Approximately 130 metabolites were significantly altered in Bcrp and P-gp knockout mice, indicating numerous metabolite-transporter interactions. We focused on BCRP specific substrates and identified riboflavin, which was significantly elevated in the plasma of Bcrp single- and Bcrp/P-gp double- but not P-gp single-knockout mice. Dual BCRP/P-gp inhibitor elacridar caused a dose-dependent increase of the area under the plasma concentration-time curve (AUC) of riboflavin in mice (1.51- and 1.93-fold increases by 30 and 150 mg/kg elacridar, respectively). In 3 cynomolgus monkeys, we observed approximately 1.7-fold increases in the riboflavin concentrations caused by ML753286 (10 mg/kg), which correlated well with the increase of sulfasalazine, a known BCRP probe in monkeys. However, the BCRP inhibitor had no effect on isobutyryl carnitine, arginine or 2-arachidonoyl glycerol levels. Additionally, clinical studies on healthy volunteers indicated low intrasubject and inter-meal variability of plasma riboflavin concentrations. In vitro experiments using membrane vesicles demonstrated riboflavin as a select substrate of monkey and human BCRP over P-gp. Collectively, this proof-of-principle study indicates that riboflavin is a suitable endogenous probe for BCRP activity in mice and monkeys and future investigation of riboflavin as a blood-based biomarker of human BCRP is warranted. Significance Statement Our results identified riboflavin as an endogenous biomarker candidate of BCRP. Its selectivity, sensitivity, and predictivity regarding BCRP inhibition have been explored. The findings of this study highlight riboflavin as an informative BCRP plasma biomarker in animal models. The utility of this biomarker requires further validation by evaluating the effects of BCRP inhibitors of different potencies on riboflavin plasma concentrations in humans. Ultimately, riboflavin may shed light on the risk assessment of BCRP DDIs in early clinical trials.PMID:37055191 | DOI:10.1124/dmd.123.001284

Restoring polyamine levels by supplementation of spermidine modulates hepatic immune landscape in murine model of NASH

Thu, 13/04/2023 - 12:00
Biochim Biophys Acta Mol Basis Dis. 2023 Apr 11:166697. doi: 10.1016/j.bbadis.2023.166697. Online ahead of print.ABSTRACTAIMS: To determine if changes in polyamines metabolism occur during non-alcoholic steatohepatitis (NASH) in human patients and mice, as well as to assess systemic and liver-specific effects of spermidine administration into mice suffering from advanced NASH.MATERIALS AND METHODS: Human fecal samples were collected from 50 healthy and 50 NASH patients. For the preclinical studies C57Bl6/N male mice fed GAN or NIH-31 diet for 6 months were ordered from Taconic and liver biopsy was performed. Based on severity of liver fibrosis, body composition and body weight, the mice from both dietary groups were randomized into another two groups: half receiving 3 mM spermidine in drinking water, half normal water for subsequent 12 weeks. Body weight was measured weekly and glucose tolerance and body composition were assessed at the end. Blood and organs were collected during necropsy, and intrahepatic immune cells were isolated for flow cytometry analysis.RESULTS: Metabolomic analysis of human and murine feces confirmed that levels of polyamines decreased along NASH progression. Administration of exogenous spermidine to the mice from both dietary groups did not affect body weight, body composition or adiposity. Moreover, incidence of macroscopic hepatic lesions was higher in NASH mice receiving spermidine. On the other hand, spermidine normalized numbers of Kupffer cells in the livers of mice suffering from NASH, although these beneficial effects did not translate into improved liver steatosis or fibrosis severity.CONCLUSION: Levels of polyamines decrease during NASH in mice and human patients but spermidine administration does not improve advanced NASH.PMID:37054999 | DOI:10.1016/j.bbadis.2023.166697

Microplastic exposure induces muscle growth but reduces meat quality and muscle physiological function in chickens

Thu, 13/04/2023 - 12:00
Sci Total Environ. 2023 Apr 11:163305. doi: 10.1016/j.scitotenv.2023.163305. Online ahead of print.ABSTRACTMicroplastic (MP) pollution has become one of the global environmental concerns, but the contamination and effect of MP on chicken skeletal muscle are scarcely researched. Here, we found MP contamination in the chicken skeletal muscles, which were directly collected from a large-scale chicken farm. Using Pyrolysis-Gas Chromatography-Mass Spectrometry and Agilent 8700 laser direct infrared imaging spectrometer, we found that polystyrene (PS) and polyamide are the significant type of MPs detected in chicken skeletal muscle. Constant PS-MP oral feeding for >21 days increases the content of MP deposited in chicken breast muscle, but the MP content in the leg muscle was gradually decreased. Surprisingly, the chicken's body and skeletal muscle weight was increased after constant PS-MP feeding. Physiological results showed that PS-MP exposure inhibited energy and lipid metabolism, induced oxidative stress, and potential for neurotoxicity in the skeletal muscle. Metabolomic analysis of the liquid chromatography-tandem mass spectrometry and gas chromatography coupled with the mass spectrometer results showed that PS-MP exposure changed the metabolomic profile and reduced meat quality. In vitro, experimental results showed that PS-MP exposure induced chicken primary myoblasts proliferation and apoptosis but decreased myoblasts differentiation. Transcriptome analysis of the skeletal muscle indicates that PS-MP exposure affects skeletal muscle function by regulating genes involved in neural function and muscle development. Considering that chicken is one of the most important meat foods in the world, this study will provide an essential reference for protecting meat food safety.PMID:37054798 | DOI:10.1016/j.scitotenv.2023.163305

DEPTOR as a novel prognostic marker inhibits the proliferation via deactivating mTOR signaling pathway in gastric cancer cells

Thu, 13/04/2023 - 12:00
Exp Cell Res. 2023 Apr 11:113598. doi: 10.1016/j.yexcr.2023.113598. Online ahead of print.ABSTRACTAberrantly activated mTOR signaling pathway is commonly found in malignancies including gastric cancer (GC). DEPTOR, as a naturally occurred inhibitor of mTOR, functions in the pro- or anti-tumor manner depending on distinct tumor contexts. However, the roles of DEPTOR in GC remain largely unknown. In this study, DEPTOR expression was identified to be significantly decreased in GC tissues compared with matched normal gastric tissues, and reduced DEPTOR level was indicative of poor prognosis in patients. Restored DEPTOR expression inhibited the propagation in AGS and NCI-N87 cells, whose DEPTOR levels are low, via deactivating mTOR signaling pathway. Likewise, cabergoline (CAB) attenuated the proliferation in AGS and NCI-N87 cells via partially rescuing DEPTOR protein level. Targeted metabolomics analysis showed that several key metabolites, such as l-serine, significantly changed in AGS cells with DEPTOR restoration. These results revealed the anti-proliferation function of DEPTOR in GC cells, suggesting that restored DEPTOR expression using CAB may be a potential therapeutic approach for patients with GC.PMID:37054772 | DOI:10.1016/j.yexcr.2023.113598

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