PubMed
Single Cell Omics of Breast Cancer: An Update on Characterization and Diagnosis.
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Single Cell Omics of Breast Cancer: An Update on Characterization and Diagnosis.
Indian J Clin Biochem. 2019 Jan;34(1):3-18
Authors: Dwivedi S, Purohit P, Misra R, Lingeswaran M, Vishnoi JR, Pareek P, Misra S, Sharma P
Abstract
Breast cancer is recognized for its different clinical behaviors and patient outcomes, regardless of common histopathological features at diagnosis. The heterogeneity and dynamics of breast cancer undergoing clonal evolution produces cells with distinct degrees of drug resistance and metastatic potential. Presently, single cell analysis have made outstanding advancements, overshadowing the hurdles of heterogeneity linked with vast populations. The speedy progression in sequencing analysis now allow unbiased, high-output and high-resolution elucidation of the heterogeneity from individual cell within a population. Classical therapeutics strategies for individual patients are governed by the presence and absence of expression pattern of the estrogen and progesterone receptors and human epidermal growth factor receptor 2. However, such tactics for clinical classification have fruitfulness in selection of targeted therapies, short-term patient responses but unable to predict the long-term survival. In any phenotypic alterations, like breast cancer disease, molecular signature have proven its implication, as we aware that individual cell's state is regulated at diverse levels, such as DNA, RNA and protein, by multifaceted interplay of intrinsic biomolecules pathways existing in the organism and extrinsic stimuli such as ambient environment. Thus for complete understanding, complete profiling of single cell requires a synchronous investigations from different levels (multi-omics) to avoid incomplete information produced from single cell. In this article, initially we briefed on novel updates of various methods available to explore omics and then we finally pinpointed on various omics (i.e. genomics, transcriptomics, epigenomics, proteomics and metabolomics) data and few special aspects of circulating tumor cells, disseminated tumor cells and cancer stem cells, so far available from various studies that can be used for better management of breast cancer patients.
PMID: 30728668 [PubMed]
Therapeutic modulation of autophagy: which disease comes first?
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Therapeutic modulation of autophagy: which disease comes first?
Cell Death Differ. 2019 Feb 06;:
Authors: Maiuri MC, Kroemer G
Abstract
The relentless efforts of thousands of researchers have allowed deciphering the molecular machinery that regulates and executes autophagy, thus identifying multiple molecular targets to enhance or block the process, rendering autophagy "druggable". Autophagy inhibition may be useful for preserving the life of cells that otherwise would succumb to excessive self-digestion. Moreover, autophagy blockade may reduce the fitness of cancer cells or interrupt metabolic circuitries required for their growth. Autophagy stimulation is probably useful for the prevention or treatment of aging, cancer (when stimulation of immunosurveillance is the therapeutic goal), cardiovascular disease, cystic fibrosis, infection by intracellular pathogens, obesity, and intoxication by heavy metals, just to mention a few examples. Epidemiological evidence suggests broad health-improving effects for lifestyles, micronutrients, and drugs that favor autophagy. In this review, we discuss the role of autophagy in disease pathogenesis while focusing on the question, which disease will become the first clinically approved indication for therapeutic autophagy modulation.
PMID: 30728461 [PubMed - as supplied by publisher]
Short-Term and Long-Term Outcomes of Infliximab and Tacrolimus Treatment for Moderate to Severe Ulcerative Colitis: Retrospective Observational Study.
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Short-Term and Long-Term Outcomes of Infliximab and Tacrolimus Treatment for Moderate to Severe Ulcerative Colitis: Retrospective Observational Study.
Kobe J Med Sci. 2018 Dec 04;64(4):E140-E148
Authors: Otsuka T, Ooi M, Tobimatsu K, Wakahara C, Watanabe D, Adachi S, Yasutomi E, Yamairi H, Ku Y, Yoshida M, Hoshi N, Kodama Y
Abstract
BACKGROUND/AIMS: While some studies have shown that IFX and TAC exhibit similar efficacy against UC in the short-term, it is unclear which drug produces better long-term outcomes. In this study, we compared the long-term efficacy of IFX and TAC in patients with moderate to severe UC.
METHODS: This retrospective study was conducted from 2009 to 2017. It included patients with no history of IFX or TAC treatment. We analyzed the clinical response and remission rates at 12 and 52 weeks, and colectomy-free and relapse-free survival were evaluated until the end of the study.
RESULTS: At 12 weeks, 94.4% and 77.8% of the patients in the IFX group (n = 18) had demonstrated clinical responses and clinical remission, respectively, whereas 72.7% of the patients in the TAC group (n = 11) exhibited clinical responses and clinical remission. The clinical response, clinical remission, and colectomy-free rates did not differ significantly between the groups. At 52 weeks, clinical responses and clinical remission had been achieved in 76.5% and 70.6% of the patients both in the IFX group, respectively. In the TAC group, clinical responses and clinical remission were achieved in 50.0% of patients. Relapse-free and colectomy-free survival were estimated significantly better in IFX group evaluated by Kaplan-Meier curves.
CONCLUSION: This study indicates that IFX and TAC produce similar short-term outcomes in UC patients, but IFX produces better long-term outcomes than TAC especially with avoidance of colectomy. Our data suggest that IFX therapy may be prioritized over TAC for the treatment of moderate to severe UC.
PMID: 30728340 [PubMed - in process]
Branched-Chain Amino Acid Catabolism Impacts Triacylglycerol Homeostasis in Chlamydomonas reinhardtii.
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Branched-Chain Amino Acid Catabolism Impacts Triacylglycerol Homeostasis in Chlamydomonas reinhardtii.
Plant Physiol. 2019 Feb 06;:
Authors: Liang Y, Kong F, Torres Romero I, Burlacot A, Cuiné S, Legeret B, Billon E, Brotman Y, Alseekh S, Fernie AR, Beisson F, Peltier G, Li-Beisson Y
Abstract
Nitrogen (N) starvation-induced triacylglycerol (TAG) synthesis and its complex relationship with starch metabolism in algal cells has been intensively studied; however, few studies have examined the interaction between amino acid metabolism and TAG biosynthesis. Here, via a forward genetic screen for TAG homeostasis, we isolated a Chlamydomonas mutant (bkdE1α) that is deficient in the E1α subunit of the branched-chain ketoacid dehydrogenase (BCKDH) complex. Metabolomics analysis revealed a defect in the catabolism of branched-chain amino acids (BCAAs) in bkdE1α. Furthermore, this mutant accumulated 30% less TAG than the parental strain during N starvation, and was compromised in TAG remobilization upon N resupply. Intriguingly, the rate of mitochondrial respiration was 20-35% lower in bkdE1α compared to the parental strains. Three additional knock-out mutants of the other components of the BCKDH complex exhibited phenotypes similar to that of bkdE1α. Transcriptional responses of BCKDH to different N statuses were consistent with its role in TAG homeostasis. Collectively, these results indicate that BCAA catabolism contributes to TAG metabolism by providing carbon precursors and ATP, thus highlighting the complex interplay between distinct subcellular metabolisms for oil storage in green microalgae.
PMID: 30728273 [PubMed - as supplied by publisher]
A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space.
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A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space.
Microbiome. 2018 09 21;6(1):171
Authors: Michelini S, Balakrishnan B, Parolo S, Matone A, Mullaney JA, Young W, Gasser O, Wall C, Priami C, Lombardo R, Kussmann M
Abstract
BACKGROUND: Weaning is a period of marked physiological change. The introduction of solid foods and the changes in milk consumption are accompanied by significant gastrointestinal, immune, developmental, and microbial adaptations. Defining a reduced number of infections as the desired health benefit for infants around weaning, we identified in silico (i.e., by advanced public domain mining) infant gut microbes as potential deliverers of this benefit. We then investigated the requirements of these bacteria for exogenous metabolites as potential prebiotic feeds that were subsequently searched for in the natural product space.
RESULTS: Using public domain literature mining and an in silico reverse metabolic approach, we constructed probiotic-prebiotic-food associations, which can guide targeted feeding of immune health-beneficial microbes by weaning food; analyzed competition and synergy for (prebiotic) nutrients between selected microbes; and translated this information into designing an experimental complementary feed for infants enrolled in a pilot clinical trial ( http://www.nourishtoflourish.auckland.ac.nz/ ).
CONCLUSIONS: In this study, we applied a benefit-oriented microbiome research strategy for enhanced early-life immune health. We extended from "classical" to molecular nutrition aiming to identify nutrients, bacteria, and mechanisms that point towards targeted feeding to improve immune health in infants around weaning. Here, we present the systems biology-based approach we used to inform us on the most promising prebiotic combinations known to support growth of beneficial gut bacteria ("probiotics") in the infant gut, thereby favorably promoting development of the immune system.
PMID: 30241567 [PubMed - indexed for MEDLINE]
Comprehensive Profiling of Fecal Metabolome of Mice by Integrated Chemical Isotope Labeling-Mass Spectrometry Analysis.
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Comprehensive Profiling of Fecal Metabolome of Mice by Integrated Chemical Isotope Labeling-Mass Spectrometry Analysis.
Anal Chem. 2018 03 06;90(5):3512-3520
Authors: Yuan BF, Zhu QF, Guo N, Zheng SJ, Wang YL, Wang J, Xu J, Liu SJ, He K, Hu T, Zheng YW, Xu FQ, Feng YQ
Abstract
Gut microbiota plays important roles in the host health. The host and symbiotic gut microbiota coproduce a large number of metabolites during the metabolism of food and xenobiotics. The analysis of fecal metabolites can provide a noninvasive manner to study the outcome of the host-gut microbiota interaction. Herein, we reported the comprehensive profiling of fecal metabolome of mice by an integrated chemical isotope labeling combined with liquid chromatography-mass spectrometry (CIL-LC-MS) analysis. The metabolites are categorized into several submetabolomes based on the functional moieties (i.e., carboxyl, carbonyl, amine, and thiol) and then analysis of the individual submetabolome was performed. The combined data from the submetabolome form the metabolome with relatively high coverage. To this end, we synthesized stable isotope labeling reagents to label metabolites with different groups, including carboxyl, carbonyl, amine, and thiol groups. We detected 2302 potential metabolites, among which, 1388 could be positively or putatively identified in feces of mice. We then further confirmed 308 metabolites based on our established library of chemically labeled standards and tandem mass spectrometry analysis. With the identified metabolites in feces of mice, we established mice fecal metabolome database, which can be used to readily identify metabolites from feces of mice. Furthermore, we discovered 211 fecal metabolites exhibited significant difference between Alzheimer's disease (AD) model mice and wild type (WT) mice, which suggests the close correlation between the fecal metabolites and AD pathology and provides new potential biomarkers for the diagnosis of AD.
PMID: 29406693 [PubMed - indexed for MEDLINE]
metabolomics; +28 new citations
28 new pubmed citations were retrieved for your search.
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metabolomics
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metabolomics; +28 new citations
28 new pubmed citations were retrieved for your search.
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metabolomics
These pubmed results were generated on 2019/02/07PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books.
Citations may include links to full-text content from PubMed Central and publisher web sites.
metabolomics; +31 new citations
31 new pubmed citations were retrieved for your search.
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metabolomics
These pubmed results were generated on 2019/02/06PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books.
Citations may include links to full-text content from PubMed Central and publisher web sites.
metabolomics; +31 new citations
31 new pubmed citations were retrieved for your search.
Click on the search hyperlink below to display the complete search results:
metabolomics
These pubmed results were generated on 2019/02/06PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books.
Citations may include links to full-text content from PubMed Central and publisher web sites.
metabolomics; +18 new citations
18 new pubmed citations were retrieved for your search.
Click on the search hyperlink below to display the complete search results:
metabolomics
These pubmed results were generated on 2019/02/05PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books.
Citations may include links to full-text content from PubMed Central and publisher web sites.
metabolomics; +18 new citations
18 new pubmed citations were retrieved for your search.
Click on the search hyperlink below to display the complete search results:
metabolomics
These pubmed results were generated on 2019/02/05PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books.
Citations may include links to full-text content from PubMed Central and publisher web sites.
Mild inborn errors of metabolism in commonly used inbred mouse strains.
Mild inborn errors of metabolism in commonly used inbred mouse strains.
Mol Genet Metab. 2019 Jan 24;:
Authors: Leandro J, Violante S, Argmann CA, Hagen J, Dodatko T, Bender A, Zhang W, Williams EG, Bachmann AM, Auwerx J, Yu C, Houten SM
Abstract
Inbred mouse strains are a cornerstone of translational research but paradoxically many strains carry mild inborn errors of metabolism. For example, α-aminoadipic acidemia and branched-chain ketoacid dehydrogenase deficiency are known in C57BL/6J mice. Using RNA sequencing, we now reveal the causal variants in Dhtkd1 and Bckdhb, and the molecular mechanism underlying these metabolic defects. C57BL/6J mice have decreased Dhtkd1 mRNA expression due to a solitary long terminal repeat (LTR) in intron 4 of Dhtkd1. This LTR harbors an alternate splice donor site leading to a partial splicing defect and as a consequence decreased total and functional Dhtkd1 mRNA, decreased DHTKD1 protein and α-aminoadipic acidemia. Similarly, C57BL/6J mice have decreased Bckdhb mRNA expression due to an LTR retrotransposon in intron 1 of Bckdhb. This transposable element encodes an alternative exon 1 causing aberrant splicing, decreased total and functional Bckdhb mRNA and decreased BCKDHB protein. Using a targeted metabolomics screen, we also reveal elevated plasma C5-carnitine in 129 substrains. This biochemical phenotype resembles isovaleric acidemia and is caused by an exonic splice mutation in Ivd leading to partial skipping of exon 10 and IVD protein deficiency. In summary, this study identifies three causal variants underlying mild inborn errors of metabolism in commonly used inbred mouse strains.
PMID: 30709776 [PubMed - as supplied by publisher]
Metabolomics assessment reveals oxidative stress and altered energy production in the heart after ischemic acute kidney injury in mice.
Metabolomics assessment reveals oxidative stress and altered energy production in the heart after ischemic acute kidney injury in mice.
Kidney Int. 2019 Jan 29;:
Authors: Fox BM, Gil HW, Kirkbride-Romeo L, Bagchi RA, Wennersten SA, Haefner KR, Skrypnyk NI, Brown CN, Soranno DE, Gist KM, Griffin BR, Jovanovich A, Reisz JA, Wither MJ, D'Alessandro A, Edelstein CL, Clendenen N, McKinsey TA, Altmann C, Faubel S
Abstract
Acute kidney injury (AKI) is a systemic disease associated with widespread effects on distant organs, including the heart. Normal cardiac function is dependent on constant ATP generation, and the preferred method of energy production is via oxidative phosphorylation. Following direct ischemic cardiac injury, the cardiac metabolome is characterized by inadequate oxidative phosphorylation, increased oxidative stress, and increased alternate energy utilization. We assessed the impact of ischemic AKI on the metabolomics profile in the heart. Ischemic AKI was induced by 22 minutes of renal pedicle clamping, and 124 metabolites were measured in the heart at 4 hours, 24 hours, and 7 days post-procedure. Forty-one percent of measured metabolites were affected, with the most prominent changes observed 24 hours post-AKI. The post-AKI cardiac metabolome was characterized by amino acid depletion, increased oxidative stress, and evidence of alternative energy production, including a shift to anaerobic forms of energy production. These metabolomic effects were associated with significant cardiac ATP depletion and with echocardiographic evidence of diastolic dysfunction. In the kidney, metabolomics analysis revealed shifts suggestive of energy depletion and oxidative stress, which were reflected systemically in the plasma. This is the first study to examine the cardiac metabolome after AKI, and demonstrates that effects of ischemic AKI on the heart are akin to the effects of direct ischemic cardiac injury.
PMID: 30709662 [PubMed - as supplied by publisher]
Metabolomic responses of mussel Mytilus galloprovincialis to fluoranthene exposure under different nutritive conditions.
Metabolomic responses of mussel Mytilus galloprovincialis to fluoranthene exposure under different nutritive conditions.
Mar Environ Res. 2019 Jan 25;:
Authors: Campillo JA, Sevilla A, González-Fernández C, Bellas J, Bernal C, Cánovas M, Albentosa M
Abstract
Biomarkers are useful tools to assess biological effects of pollutants that are extensively used in monitoring programs to assess ecosystem health. However, they are strongly affected by mussel physiological state, especially nutritive status, which has led to the search of new biological indicators of chemical pollutants exposition. Environmental metabolomics is an approach for examining the metabolic responses (measurement of low molecular weight endogenous metabolites) of an organism to both natural and anthropogenic stressors that can occur in its environment. The aim of the present work was to assess the effect of the polycyclic aromatic hydrocarbon fluoranthene (FLU) exposure on the metabolomic profiles of mussel digestive glands under different nutritive conditions. To achieve this objective, mussels were reared, for a period of 56 days, under three different food rations in order to obtain a gradient of nutritive status (negative, zero and positive energy balance), and after that, they were exposed, during 3 weeks, to a nominal concentration of 3 μg FLU L-1. A total of 43 metabolites, including aminoacids (Ala, Val, Leu, Ile, etc.), energy metabolism related metabolites (ATP, AMP, etc.), organic osmolytes (taurine, etc.), redox metabolism (GSH, NADP+) and nucleotides, were identified and quantified in the digestive glands of the mussels. Principal Component Analysis (PCA) defined two principal components (PC1 and PC2) that explained 55.6% of the total variance, although the first component explains more than 80% of this variance, this being related to the mussel nutritive condition. The effect of the toxicant, explained by the PC2, is similar to that produced under conditions of food restriction, which masks the effect of the toxicant under these conditions. As the feeding conditions are more favorable, the toxic effect becomes more apparent. Therefore, the great influence of nutritive condition on mussel metabolome implies a handicap for the use of metabolomic biomarkers, as previously demonstrated for biochemical and other molecular biomarkers, in large-scale monitoring programs in which several food conditions coexist with pollution levels.
PMID: 30709639 [PubMed - as supplied by publisher]
Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae.
Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae.
Microb Cell Fact. 2019 Feb 01;18(1):25
Authors: Bergman A, Hellgren J, Moritz T, Siewers V, Nielsen J, Chen Y
Abstract
INTRODUCTION: Phosphoketolases (Xfpk) are a non-native group of enzymes in yeast, which can be expressed in combination with other metabolic enzymes to positively influence the yield of acetyl-CoA derived products by reducing carbon losses in the form of CO2. In this study, a yeast strain expressing Xfpk from Bifidobacterium breve, which was previously found to have a growth defect and to increase acetate production, was characterized.
RESULTS: Xfpk-expression was found to increase respiration and reduce biomass yield during glucose consumption in batch and chemostat cultivations. By cultivating yeast with or without Xfpk in bioreactors at different pHs, we show that certain aspects of the negative growth effects coupled with Xfpk-expression are likely to be explained by proton decoupling. At low pH, this manifests as a reduction in biomass yield and growth rate in the ethanol phase. Secondly, we show that intracellular sugar phosphate pools are significantly altered in the Xfpk-expressing strain. In particular a decrease of the substrates xylulose-5-phosphate and fructose-6-phosphate was detected (26% and 74% of control levels) together with an increase of the products glyceraldehyde-3-phosphate and erythrose-4-phosphate (208% and 542% of control levels), clearly verifying in vivo Xfpk enzymatic activity. Lastly, RNAseq analysis shows that Xfpk expression increases transcription of genes related to the glyoxylate cycle, the TCA cycle and respiration, while expression of genes related to ethanol and acetate formation is reduced. The physiological and transcriptional changes clearly demonstrate that a heterologous phosphoketolase flux in combination with endogenous hydrolysis of acetyl-phosphate to acetate increases the cellular demand for acetate assimilation and respiratory ATP-generation, leading to carbon losses.
CONCLUSION: Our study shows that expression of Xfpk in yeast diverts a relatively small part of its glycolytic flux towards acetate formation, which has a significant impact on intracellular sugar phosphate levels and on cell energetics. The elevated acetate flux increases the ATP-requirement for ion homeostasis and need for respiratory assimilation, which leads to an increased production of CO2. A majority of the negative growth effects coupled to Xfpk expression could likely be counteracted by preventing acetate accumulation via direct channeling of acetyl-phosphate towards acetyl-CoA.
PMID: 30709397 [PubMed - in process]
Evaluation of the Hepatotoxicity of the Zhi-Zi-Hou-Po Decoction by Combining UPLC-Q-Exactive-MS-Based Metabolomics and HPLC-MS/MS-Based Geniposide Tissue Distribution.
Evaluation of the Hepatotoxicity of the Zhi-Zi-Hou-Po Decoction by Combining UPLC-Q-Exactive-MS-Based Metabolomics and HPLC-MS/MS-Based Geniposide Tissue Distribution.
Molecules. 2019 Jan 31;24(3):
Authors: Wang Y, Feng F
Abstract
With traditional Chinese medicine (TCM) becoming widespread globally, its safety has increasingly become a concern, especially its hepatoxicity. For example, Gardenia jasminoides Ellis is a key ingredient in the Zhi-Zi-Hou-Po decoction (ZZHPD), which is a commonly-used clinically combined prescription of TCM that may induce hepatoxicity. However, the underlying toxicity mechanism of ZZHPD is not fully understood. In this study, a plasma metabolomics strategy was used to investigate the mechanism of ZZHPD-induced hepatotoxicity through profiling entire endogenous metabolites. Twenty-four Sprague-Dawley rats were randomly assigned into four groups, which were orally administered with 0.9% saline, as well as 2.7 g/kg/day, 8.1 g/kg/day, or 27 g/kg/day of ZZHPD for 30 consecutive days, respectively. Biochemical assay and metabolomics assay were used to detect serum and plasma samples, whilst histopathological assay was used for detecting liver tissues, and the geniposide distribution in tissues was simultaneously measured. The results showed that the concentration of 20 metabolites linked to amino acid, lipid, and bile acid metabolism had significant changes in the ZZHPD-treated rats. Moreover, toxic effects were aggravated with serum biochemical and histopathological examines in liver tissues as the dosage increased, which may be associated with the accumulation of geniposide in the liver as the dosage increased. Notably, our findings also demonstrated that the combined metabolomics strategy with tissue distribution had significant potential for elucidating the mechanistic complexity of the toxicity of TCM.
PMID: 30708983 [PubMed - in process]
metabolomics; +16 new citations
16 new pubmed citations were retrieved for your search.
Click on the search hyperlink below to display the complete search results:
metabolomics
These pubmed results were generated on 2019/02/02PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books.
Citations may include links to full-text content from PubMed Central and publisher web sites.
Interaction of Clopidogrel and Fufang Danshen Dripping Pills Assay in Coronary Heart Disease based on Non-target Metabolomics.
Related Articles
Interaction of Clopidogrel and Fufang Danshen Dripping Pills Assay in Coronary Heart Disease based on Non-target Metabolomics.
J Ethnopharmacol. 2019 Jan 28;:
Authors: Mengzhe G, Tianyun W, Jian Y, Chang H, Ji S, Daoquan T
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE: Clopidogrel is the recommended treatment by current clinical practice guidelines to prevent adverse cardiovascular events in patients with coronary heart disease (CHD), but this treatment regimen still fails and 5%-40% patients display inadequate antiplatelet responses. Fufang Danshen Dripping Pill (FDDP) was used as the combination with clopidogrel to improve the therapeutic effect. However, the mechanism of the interaction between clopidogrel and FDDP has not been elucidated.
MATERIALS AND METHODS: We have used non-targeted metabolism method based on GC-MS and LC-MS for the investigation of drug interactions between clopidogrel and FDDP. 63 patients were divided into four groups with different dosage regimen and the serum samples were collected for the analysis.
RESULTS: We have found 5 and 55 differential metabolites between health volunteer group and CHD patients group, respectively. The contents of these differential metabolites had diverse changes in clopidogrel group, FDDP group, and drug combination group, indicating that the clopidogrel and FDDP combination can adjust the glycometabolism, lipid metabolism, and phospholipid metabolism, sequentially made the content of downstream related metabolites towards to the health volunteer group.
CONCLUSION: This work has explained the mechanism of the interaction between clopidogrel and FDDP from the point of view of metabolic product change, and revealed the potential metabolic pathways it affects, which provided the new ideas for clinical medication.
PMID: 30703494 [PubMed - as supplied by publisher]
Comprehensive and empirical evaluation of machine learning algorithms for small molecule LC retention time prediction.
Related Articles
Comprehensive and empirical evaluation of machine learning algorithms for small molecule LC retention time prediction.
Anal Chem. 2019 Jan 31;:
Authors: Bouwmeester R, Martens L, Degroeve S
Abstract
Liquid chromatography is a core component of almost all mass spectrometric analyses of (bio)molecules. Because of the high-throughput nature of mass spectrometric analyses, the interpretation of these chromatographic data increasingly relies on informatics solutions that attempt to predict an analyte's retention time. The key components of such predictive algorithms are the features these are supplies with, and the actual machine learning algorithm used to fit the model parameters. Therefore, we have evaluated the performance of seven machine learning algorithms on 36 distinct metabolomics data sets, using two distinct feature sets. Interestingly, the results show that no single learning algorithm performs optimally for all data sets, with different types of algorithms achieving top performance for different types of analytes or different protocols. Our results thus show that an evaluation of machine learning algorithms for retention time prediction is needed to find a suitable algorithm for specific analytes or protocols. Importantly, however, our results also show that blending different types of models together decreases the error on outliers, indicating that the combination of several approaches holds substantial promise for the development of more generic, high-performing algorithms.
PMID: 30702864 [PubMed - as supplied by publisher]