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

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 40 min 54 sec ago

Epigenetic events involved in OCT1-dependent impaired response of hepatocellular carcinoma to sorafenib.

Sun, 30/12/2018 - 04:13
Epigenetic events involved in OCT1-dependent impaired response of hepatocellular carcinoma to sorafenib. Br J Pharmacol. 2018 Dec 28;: Authors: Al-Abdulla R, Lozano E, Macias RIR, Monte MJ, Briz O, O'Rourke CJ, Serrano MA, Banales JM, Avila MA, Martinez-Chantar ML, Geier A, Andersen JB, Marin JJG Abstract BACKGROUND AND PURPOSE: In hepatocellular carcinoma (HCC), the expression of the human organic cation transporter-1 (hOCT1, gene SLC22A1) is reduced. The molecular bases of this phenotypic characteristic and the relationship with the poor response of HCC to sorafenib were investigated. EXPERIMENTAL APPROACH AND KEY RESULTS: hOCT1 over-expression in human hepatoma cells (HuH7 and HepG2) enhanced sorafenib, but not regorafenib, uptake in a quinine sensitive manner. The analysis of HCC transcriptomes (TCGA, n=366) showed reduced hOCT1 mRNA, which was inversely correlated with SLC22A1 promoter methylation. The demethylating agent decitabine enhanced hOCT1 expression in hepatoma cells. In clinical samples of HCC, determination of total and alternatively spliced hOCT1 mRNA transcripts revealed enhanced proportion of aberrant short variants. Six miRNAs highly expressed in HCC (TCGA) were identified by in silico analysis as candidates to target hOCT1 mRNA. When overexpressed in HepG2 cells a significant hOCT1 mRNA decay was induced only by hsa-mir-330 and hsa-mir-1468. Analysis of 39 paired samples from TCGA revealed that only hsa-mir-330 was consistently up-regulated in HCC. The expression of the orthologues mOct1 and rOct1 was reduced in spontaneously generated HCC in Fxr-/- mice and chemically induced HCC in rats, respectively. This resulted in impaired uptake of sorafenib (HPLC-MS/MS). In mice, sorafenib treatment efficiently inhibited the growth of subcutaneously implanted tumours only if these were generated by cells over-expressing hOCT1. CONCLUSION AND IMPLICATIONS: Impaired hOCT1 expression/function in HCC, which is due in part to epigenetic modifications, plays an important role in the poor pharmacological response of this cancer to sorafenib. PMID: 30592786 [PubMed - as supplied by publisher]

Discriminating high-risk cervical Human Papilloma Virus infections with urinary biomarkers via non-targeted GC-MS-based metabolomics.

Sun, 30/12/2018 - 04:13
Discriminating high-risk cervical Human Papilloma Virus infections with urinary biomarkers via non-targeted GC-MS-based metabolomics. PLoS One. 2018;13(12):e0209936 Authors: Godoy-Vitorino F, Ortiz-Morales G, Romaguera J, Sanchez MM, Martinez-Ferrer M, Chorna N Abstract Genital human papillomavirus (HPV) is the world's most commonly diagnosed sexually transmitted infection, and high-risk HPV types are strongly linked to cervical dysplasia and carcinoma. Puerto Ricans are among the US citizens with higher HPV prevalence and lower screening rates and access to treatment. This bleak statistic was as a motivation to detect biomarkers for early diagnosis of HPV in this population. We collected both urine and cervical swabs from 43 patients attending San Juan Clinics. Cervical swabs were used for genomic DNA extractions and HPV genotyping with the HPV SPF10-LiPA25 kit, and gas chromatography-mass spectrometry (GC-MS) was employed on the urine-derived products for metabolomics analyses. We aimed at discriminating between patients with different HPV categories: HPV negative (HPV-), HPV positive with simultaneous low and high-risk infections (HPV+B) and HPV positive exclusively high-risk (HPV+H). We found that the metabolome of HPV+B is closer to HPV- than to HPV+H supporting evidence that suggests HPV co-infections may be antagonistic due to viral interference leading to a lower propensity for cervical cancer development. In contrast, metabolites of patients with HPV+H were significantly different from those that were HPV-. We identified three urinary metabolites 5-Oxoprolinate, Erythronic acid and N-Acetylaspartic acid that discriminate HPV+H cases from negative controls. These metabolites are known to be involved in a variety of biochemical processes related to energy and metabolism and may likely be biomarkers for HPV high-risk cervical infection. However, further validation should follow using a larger patient cohort and diverse populations to confirm our finding. PMID: 30592768 [PubMed - in process]

Tissue-specific metabolomics analysis identifies the liver as a major organ of metabolic disorders in amyloid precursor protein/presenilin 1 (APP/PS1) mice of Alzheimer's disease.

Sun, 30/12/2018 - 04:13
Tissue-specific metabolomics analysis identifies the liver as a major organ of metabolic disorders in amyloid precursor protein/presenilin 1 (APP/PS1) mice of Alzheimer's disease. J Proteome Res. 2018 Dec 28;: Authors: Zheng H, Cai A, Shu Q, Niu Y, Xu P, Li C, Lin L, Gao H Abstract Alzheimer's disease (AD) is regarded as a metabolic disorder and more attention has been paid to brain metabolism. However, AD may also affect metabolism in the peripheral organs beyond the brain. In this study, therefore, we investigated metabolic changes in the liver, kidney and heart of amyloid precursor protein/presenilin 1 (APP/PS1) mice at 1, 5 and 10 months of age by using 1H NMR-based metabolomics and chemometrics. Metabolomic results reveal that the liver was the earliest affected organ in APP/PS1 mice during amyloid pathology progression, followed by the kidney and heart. Moreover, a hypometabolic state was found in the liver of APP/PS1 mice at 5 months of age, and the disturbed metabolites were mainly involved in energy metabolism, amino acid metabolism, nucleic acid metabolism as well as ketone and fatty acid metabolism. In conclusion, our results suggest that AD is a systemic metabolic dysfunction and hepatic metabolic abnormality may reflect amyloid pathology progression. PMID: 30592618 [PubMed - as supplied by publisher]

Targeted metabolomics of sulfated bile acids in urine for the diagnosis and grading of intrahepatic cholestasis of pregnancy.

Sun, 30/12/2018 - 04:13
Related Articles Targeted metabolomics of sulfated bile acids in urine for the diagnosis and grading of intrahepatic cholestasis of pregnancy. Genes Dis. 2018 Dec;5(4):358-366 Authors: Li Y, Zhang X, Chen J, Feng C, He Y, Shao Y, Ding M Abstract Intrahepatic cholestasis of pregnancy (ICP) is related to cholestatic disorder in pregnancy. Total urinary sulfated bile acids (SBAs) were found increased in ICP. We distinguished the metabolic profiling of urinary SBAs in ICP to find potential biomarkers for the diagnosis and grading of ICP. The targeted metabolomics based on high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was used to analyze urinary SBAs profiling in mild and severe ICP cases, as well as healthy controls. 16 kinds of urinary SBAs were determined by HPLC-MS/MS. Sulfated dihydroxy glycine bile acid (di-GBA-S), glycine cholic acid 3-sulfate (GCA-3S), sulfated dihydroxy taurine bile acid (di-TBA-S) and taurine cholic acid 3-sulfate (TCA-3S) increased significantly in ICP group compared with the control group. Seven kinds of SBAs were significantly different (p < 0.05) between the ICP group and the control group, with the variable importance in the projection (VIP) value more than one by the orthogonal partial least squares discriminant analysis (OPLS-DA). GCA-3S was well-suited to be used as the biomarker for the diagnosis of ICP with the sensitivity of 100% and specificity of 95.5%. A multi-variable logistic regression containing GCA-3S and di-GBA-S-1 was constructed to distinguish severe ICP from mild ICP, with the sensitivity of 94.4% and specificity of 100%. The developed HPLC-MS/MS method is suitable for the measurement of urinary SBAs profiling. Moreover, the urinary SBAs in the metabolomic profiling have the potential to be used as non-intrusive biomarkers for the diagnosis and grading of ICP. PMID: 30591938 [PubMed]

Low-Field, Benchtop NMR Spectroscopy as a Potential Tool for Point-of-Care Diagnostics of Metabolic Conditions: Validation, Protocols and Computational Models.

Sun, 30/12/2018 - 04:13
Related Articles Low-Field, Benchtop NMR Spectroscopy as a Potential Tool for Point-of-Care Diagnostics of Metabolic Conditions: Validation, Protocols and Computational Models. High Throughput. 2018 Dec 27;8(1): Authors: Percival BC, Grootveld M, Gibson M, Osman Y, Molinari M, Jafari F, Sahota T, Martin M, Casanova F, Mather ML, Edgar M, Masania J, Wilson PB Abstract Novel sensing technologies for liquid biopsies offer promising prospects for the early detection of metabolic conditions through omics techniques. Indeed, high-field nuclear magnetic resonance (NMR) facilities are routinely used for metabolomics investigations on a range of biofluids in order to rapidly recognise unusual metabolic patterns in patients suffering from a range of diseases. However, these techniques are restricted by the prohibitively large size and cost of such facilities, suggesting a possible role for smaller, low-field NMR instruments in biofluid analysis. Herein we describe selected biomolecule validation on a low-field benchtop NMR spectrometer (60 MHz), and present an associated protocol for the analysis of biofluids on compact NMR instruments. We successfully detect common markers of diabetic control at low-to-medium concentrations through optimised experiments, including α-glucose (≤2.8 mmol/L) and acetone (25 µmol/L), and additionally in readily accessible biofluids, particularly human urine. We present a combined protocol for the analysis of these biofluids with low-field NMR spectrometers for metabolomics applications, and offer a perspective on the future of this technique appealing to 'point-of-care' applications. PMID: 30591692 [PubMed]

Metabolomics and Age-Related Macular Degeneration.

Sun, 30/12/2018 - 04:13
Related Articles Metabolomics and Age-Related Macular Degeneration. Metabolites. 2018 Dec 27;9(1): Authors: Brown CN, Green BD, Thompson RB, den Hollander AI, Lengyel I, EYE-RISK consortium Abstract Age-related macular degeneration (AMD) leads to irreversible visual loss, therefore, early intervention is desirable, but due to its multifactorial nature, diagnosis of early disease might be challenging. Identification of early markers for disease development and progression is key for disease diagnosis. Suitable biomarkers can potentially provide opportunities for clinical intervention at a stage of the disease when irreversible changes are yet to take place. One of the most metabolically active tissues in the human body is the retina, making the use of hypothesis-free techniques, like metabolomics, to measure molecular changes in AMD appealing. Indeed, there is increasing evidence that metabolic dysfunction has an important role in the development and progression of AMD. Therefore, metabolomics appears to be an appropriate platform to investigate disease-associated biomarkers. In this review, we explored what is known about metabolic changes in the retina, in conjunction with the emerging literature in AMD metabolomics research. Methods for metabolic biomarker identification in the eye have also been discussed, including the use of tears, vitreous, and aqueous humor, as well as imaging methods, like fluorescence lifetime imaging, that could be translated into a clinical diagnostic tool with molecular level resolution. PMID: 30591665 [PubMed]

Mechanism of Curcuma wenyujin Rhizoma on Acute Blood Stasis in Rats Based on a UPLC-Q/TOF-MS Metabolomics and Network Approach.

Sun, 30/12/2018 - 04:13
Related Articles Mechanism of Curcuma wenyujin Rhizoma on Acute Blood Stasis in Rats Based on a UPLC-Q/TOF-MS Metabolomics and Network Approach. Molecules. 2018 Dec 27;24(1): Authors: Hao M, Ji, Li L, Su L, Gu W, Gu L, Wang Q, Lu T, Mao C Abstract Rhizome of Curcuma wenyujin, which is called EZhu in China, is a traditional Chinese medicine used to treat blood stasis for many years. However, the underlying mechanism of EZhu is not clear at present. In this study, plasma metabolomics combined with network pharmacology were used to elucidate the therapeutic mechanism of EZhu in blood stasis from a metabolic perspective. The results showed that 26 potential metabolite markers of acute blood stasis were screened, and the levels were all reversed to different degrees by EZhu preadministration. Metabolic pathway analysis showed that the improvement of blood stasis by Curcuma wenyujin rhizome was mainly related to lipid metabolism (linoleic acid metabolism, ether lipid metabolism, sphingolipid metabolism, glycerophospholipid metabolism, and arachidonic acid metabolism) and amino acid metabolisms (tryptophan metabolism, lysine degradation). The component-target-pathway network showed that 68 target proteins were associated with 21 chemical components in EZhu. Five metabolic pathways of the network, including linoleic acid metabolism, sphingolipid metabolism, glycerolipid metabolism, arachidonic acid metabolism, and steroid hormone biosynthesis, were consistent with plasma metabolomics results. In conclusion, plasma metabolomics combined with network pharmacology can be helpful to clarify the mechanism of EZhu in improving blood stasis and to provide a literature basis for further research on the therapeutic mechanism of EZhu in clinical practice. PMID: 30591632 [PubMed - in process]

Metabolomics-based Discovery of Serum Biomarkers to Predict the Side-effects of Neoadjuvant Chemoradiotherapy for Esophageal Squamous Cell Carcinoma.

Sun, 30/12/2018 - 04:13
Related Articles Metabolomics-based Discovery of Serum Biomarkers to Predict the Side-effects of Neoadjuvant Chemoradiotherapy for Esophageal Squamous Cell Carcinoma. Anticancer Res. 2019 Jan;39(1):519-526 Authors: Nishiumi S, Fujigaki S, Kobayashi T, Kojima T, Ito Y, Daiko H, Kato K, Shoji H, Kodama Y, Honda K, Yoshida M Abstract BACKGROUND/AIM: Neoadjuvant chemoradiotherapy has side-effects that adversely affect patients' quality of life. The aim of this study was to identify serum metabolite biomarkers that might be used to predict the side-effects of neoadjuvant chemoradiotherapy for esophageal squamous cell carcinoma (ESCC). PATIENTS AND METHODS: Metabolomic analysis of serum samples from 26 patients with ESCC that were collected before neoadjuvant chemoradiotherapy was performed. The metabolites associated with hematological toxicity or nephrotoxicity were evaluated. RESULTS: Serum levels of glutaric acid, glucuronic acid, and cystine were significantly higher in hematological toxicity, and phosphatidylcholines and phosphatidylethanolamines exhibited a tendency to be higher in those with hematological toxicity. The serum level of pyruvic acid was significantly lower in nephrotoxicity, and lysophosphatidylcholines and lysophosphatidylethanolamines tended to be lower in those with nephrotoxicity. CONCLUSION: Our study found that serum levels of some metabolites differed significantly between patients with and without hematological or renal side-effects. These metabolites may be useful biomarkers for predicting hematological toxicity or nephrotoxicity after neoadjuvant chemoradiotherapy for ESCC. PMID: 30591504 [PubMed - in process]

Identification of a natural inhibitor of methionine adenosyltransferase 2A regulating one-carbon metabolism in keratinocytes.

Sun, 30/12/2018 - 04:13
Related Articles Identification of a natural inhibitor of methionine adenosyltransferase 2A regulating one-carbon metabolism in keratinocytes. EBioMedicine. 2018 Dec 24;: Authors: Bai J, Gao Y, Chen L, Yin Q, Lou F, Wang Z, Xu Z, Zhou H, Li Q, Cai W, Sun Y, Niu L, Wang H, Wei Z, Lu S, Zhou A, Zhang J, Wang H Abstract BACKGROUND: Psoriasis is a common chronic inflammatory skin disease which lacks effective strategies for the treatment. Natural compounds with biological activities are good tools to identify new targets with therapeutic potentials. Acetyl-11-keto-β-boswellic acid (AKBA) is the most bioactive ingredient of boswellic acids, a group of compounds with anti-inflammatory and anti-cancer properties. Target identification of AKBA and metabolomics analysis of psoriasis helped to elucidate the molecular mechanism underlying its effect, and provide new target(s) to treat the disease. METHODS: To explore the targets and molecular mechanism of AKBA, we performed affinity purification, metabolomics analysis of HaCaT cells treated with AKBA, and epidermis of imiquimod (IMQ) induced mouse model of psoriasis and psoriasis patients. FINDINGS: AKBA directly interacts with methionine adenosyltransferase 2A (MAT2A), inhibited its enzyme activity, decreased level of S-adenosylmethionine (SAM) and SAM/SAH ratio, and reprogrammed one‑carbon metabolism in HaCaT cells. Untargeted metabolomics of epidermis showed one‑carbon metabolism was activated in psoriasis patients. Topical use of AKBA improved inflammatory phenotype of IMQ induced psoriasis-like mouse model. Molecular docking and site-directed mutagenesis revealed AKBA bound to an allosteric site at the interface of MAT2A dimer. INTERPRETATION: Our study extends the molecular mechanism of AKBA by revealing a new interacting protein MAT2A. And this leads us to find out the dysregulated one‑carbon metabolism in psoriasis, which indicates the therapeutic potential of AKBA in psoriasis. FUND: The National Natural Science Foundation, the National Program on Key Basic Research Project, the Shanghai Municipal Commission, the Leading Academic Discipline Project of the Shanghai Municipal Education Commission. PMID: 30591370 [PubMed - as supplied by publisher]

Transcriptomics and metabonomics analyses of maternal DEHP exposure on male offspring.

Sun, 30/12/2018 - 04:13
Related Articles Transcriptomics and metabonomics analyses of maternal DEHP exposure on male offspring. Environ Sci Pollut Res Int. 2018 Sep;25(26):26322-26329 Authors: Zhang Y, Zhang W, Fu X, Zhou F, Yu H, Na X Abstract The objectives of this study were to evaluate the effect of maternal Di-2-ethylhexyl phthalate (DEHP) exposure on male offspring and to explore the mechanism of changes with the metabolic alterations and differential genes. Pregnant female Sprague-Dawley (SD) rats were intragastrically administered with 600 mg/kg body weight of DEHP or corn oil (CON) throughout pregnancy and lactation. The growth of male offspring was investigated until 14 weeks old, the indices of blood were detected, and mechanism was studied using metabonomics and transcriptomics. Compared with the CON group, body weight, body length, food intake, body fat weight, Lee's index, organ coefficient, blood lipids, and oral glucose tolerance test (OGTT) of male offspring were not significantly changed in maternal DEHP group. However, serum biochemical indexes such as alanine transaminase (ALT), total protein (TP), albumin (ALB), blood urea nitrogen (BUN), and creatinine (CREA) were markedly reduced in maternal DEHP group (p < 0.05). In addition, insulin level was elevated and catalase (CAT) level was decreased notably in maternal DEHP group compared with the CON group (p < 0.05). Furthermore, thyroxine (T4) level was lower and thyroid stimulating hormone (TSH) level was higher in maternal DEHP group (p < 0.05). Metabonomics revealed seven principal metabolites were identified, including increased L-allothreonine, creatine, uric acid, retinyl ester, L-palmitoylcarnitine, and decreased glycocholic acid and LysoPC (18:3). Transcriptomics displayed 35 differential genes were involved in the mechanism of maternal DEHP exposure. Therefore, this research confirms the effect of a certain dose of maternal DEHP exposure on male offspring and understands exactly the mechanism of these changes with metabonomics and transcriptomics. PMID: 29978319 [PubMed - indexed for MEDLINE]

Bayesian inference of networks across multiple sample groups and data types.

Fri, 28/12/2018 - 12:43
Bayesian inference of networks across multiple sample groups and data types. Biostatistics. 2018 Dec 26;: Authors: Shaddox E, Peterson CB, Stingo FC, Hanania NA, Cruickshank-Quinn C, Kechris K, Bowler R, Vannucci M Abstract In this article, we develop a graphical modeling framework for the inference of networks across multiple sample groups and data types. In medical studies, this setting arises whenever a set of subjects, which may be heterogeneous due to differing disease stage or subtype, is profiled across multiple platforms, such as metabolomics, proteomics, or transcriptomics data. Our proposed Bayesian hierarchical model first links the network structures within each platform using a Markov random field prior to relate edge selection across sample groups, and then links the network similarity parameters across platforms. This enables joint estimation in a flexible manner, as we make no assumptions on the directionality of influence across the data types or the extent of network similarity across the sample groups and platforms. In addition, our model formulation allows the number of variables and number of subjects to differ across the data types, and only requires that we have data for the same set of groups. We illustrate the proposed approach through both simulation studies and an application to gene expression levels and metabolite abundances on subjects with varying severity levels of chronic obstructive pulmonary disease. Bayesian inference; Chronic obstructive pulmonary disease (COPD); Data integration; Gaussian graphical model; Markov random field prior; Spike and slab prior. PMID: 30590505 [PubMed - as supplied by publisher]

An alternative to mineral phosphorus fertilizers: The combined effects of Trichoderma harzianum and compost on Zea mays, as revealed by 1H NMR and GC-MS metabolomics.

Fri, 28/12/2018 - 12:43
An alternative to mineral phosphorus fertilizers: The combined effects of Trichoderma harzianum and compost on Zea mays, as revealed by 1H NMR and GC-MS metabolomics. PLoS One. 2018;13(12):e0209664 Authors: Vinci G, Cozzolino V, Mazzei P, Monda H, Spaccini R, Piccolo A Abstract The ability of Trichoderma harzianum (strain OMG-08) as plant growth promoting fungus (PGPF), was tested on Zea mays plants grown in soil pots added with different inorganic (triple superphosphate and rock phosphate) and organic (cow and horse manure composts) P fertilizers. The effect of treatments was evaluated by following the variations of plants dry biomass and nutrient content, as well as the metabolic changes in plant leaves by both GC-MS and NMR spectroscopy. A synergic effect was observed in treatments with both composts and fungus inoculation, in which not only plant growth and P uptake were enhanced, but also the expression of different metabolites related to an improved photosynthetic activity. Conversely, the combination of Trichoderma with inorganic fertilizers was less effective and even showed a reduction of plants shoot biomass and N content. The corresponding plant metabolome revealed metabolic compounds typical of biotic or abiotic stresses, which may be attributed to a reduced capacity of inorganic fertilizers to provide a sufficient P availability during plant growth. Our findings also indicate that the molecular composition of compost differentiated the Trichoderma activity in sustaining plant growth. The positive effects of the combined Trichoderma and compost treatment suggest that it may become an alternative to the phosphorus mineral fertilization. PMID: 30589863 [PubMed - in process]

Revealing Different Lung Metastatic Potentials Induced Metabolic Alterations of Hepatocellular Carcinoma Cells via Proton Nuclear Magnetic Resonance Spectroscopy.

Fri, 28/12/2018 - 12:43
Related Articles Revealing Different Lung Metastatic Potentials Induced Metabolic Alterations of Hepatocellular Carcinoma Cells via Proton Nuclear Magnetic Resonance Spectroscopy. J Cancer. 2018;9(24):4696-4705 Authors: Chen Y, Lin D, Chen Z, Feng J, Liao N Abstract Background: Hepatocellular carcinoma (HCC) causes death mainly by disseminated metastasis progression and major challenge of clinical management is to distinguish lethal metastatic stage from indolent stage. It is shown that metastatic progression is closely related to cellular metabolism. But detailed metabolic alterations and molecular mechanisms still kept unclear between subtypes of different lung metastatic potentials. Methods: The current work used NMR-based metabolomics in the study of HCC cells with high malignancy but differed in lung metastatic potentials. Cell extracts and cultured media from MHCC97L and MHCC97H were utilized to reveal metabolic alterations related to metastatic potentials. Multivariate analyses were performed to identify characteristic metabolites which were used subsequently to draw the map of relative biochemical pathways by combining KEGG database. Results: The NMR spectra of both MHCC97L and MHCC97H include various signals from necessary nutritional components and metabolic intermediates. A series of characteristic metabolites were determined from both cell extracts and media. The ability on nutrient uptake varied from cell lines. Most of amino acids decreased in high metastatic cell line, so altered amino acid metabolisms and energy metabolism were revealed in high metastatic MHCC97H cell line. The majority pathways involved six essential amino acids in which the observed branched-chain amino acids together with lysine contributed to biosynthesis or degradation. Basically MHCC97H cell line could induce more active events than that of MHCC97L to progress to high metastasis with certain molecular events. Characteristic metabolites-derived classifiers performed robustly during prediction and confirmed their critical role in supporting metastasis progression. Conclusions: Our results provide evidence that NMR-metabolomics analyses of cells are able to understand metastatic characteristics accountable for biological properties. The proposed characteristic metabolites will help to understand HCC metastatic characterizations and may be filtered as potential biomarkers. PMID: 30588254 [PubMed]

Analysis of repeated leukocyte DNA methylation assessments reveals persistent epigenetic alterations after an incident myocardial infarction.

Fri, 28/12/2018 - 12:43
Related Articles Analysis of repeated leukocyte DNA methylation assessments reveals persistent epigenetic alterations after an incident myocardial infarction. Clin Epigenetics. 2018 Dec 27;10(1):161 Authors: Ward-Caviness CK, Agha G, Chen BH, Pfeiffer L, Wilson R, Wolf P, Gieger C, Schwartz J, Vokonas PS, Hou L, Just AC, Bandinelli S, Hernandez DG, Singleton AB, Prokisch H, Meitinger T, Kastenmüller G, Ferrucci L, Baccarelli AA, Waldenberger M, Peters A Abstract BACKGROUND: Most research into myocardial infarctions (MIs) have focused on preventative efforts. For survivors, the occurrence of an MI represents a major clinical event that can have long-lasting consequences. There has been little to no research into the molecular changes that can occur as a result of an incident MI. Here, we use three cohorts to identify epigenetic changes that are indicative of an incident MI and their association with gene expression and metabolomics. RESULTS: Using paired samples from the KORA cohort, we screened for DNA methylation loci (CpGs) whose change in methylation is potentially indicative of the occurrence of an incident MI between the baseline and follow-up exams. We used paired samples from the NAS cohort to identify 11 CpGs which were predictive in an independent cohort. After removing two CpGs associated with medication usage, we were left with an "epigenetic fingerprint" of MI composed of nine CpGs. We tested this fingerprint in the InCHIANTI cohort where it moderately discriminated incident MI occurrence (AUC = 0.61, P = 6.5 × 10-3). Returning to KORA, we associated the epigenetic fingerprint loci with cis-gene expression and integrated it into a gene expression-metabolomic network, which revealed links between the epigenetic fingerprint CpGs and branched chain amino acid (BCAA) metabolism. CONCLUSIONS: There are significant changes in DNA methylation after an incident MI. Nine of these CpGs show consistent changes in multiple cohorts, significantly discriminate MI in independent cohorts, and were independent of medication usage. Integration with gene expression and metabolomics data indicates a link between MI-associated epigenetic changes and BCAA metabolism. PMID: 30587240 [PubMed - in process]

MS-based metabolomics revealing Bornean Sinularia sp. extract dysregulated lipids triggering programmed cell death in Hepatocellular carcinoma.

Fri, 28/12/2018 - 12:43
Related Articles MS-based metabolomics revealing Bornean Sinularia sp. extract dysregulated lipids triggering programmed cell death in Hepatocellular carcinoma. Nat Prod Res. 2018 Dec 26;:1-8 Authors: Ling YS, Lim LR, Yong YS, Tamin O, Puah PY Abstract Soft coral, Sinularia sp. had been proven to inherit promising anti-cancer properties against variety of cancer. Current study, Sinularia sp. extract was introduced to Hepatocellular carcinoma (Hep 3B). Cell viability assay indicated the extract exhibit a dose and time dependent cytotoxicity. LC50 exhibited the lowest at 72 h post treatment estimated as 45.3 µg/mL. Morphological alterations including nuclear condensation, cytoplasm shrinkage and deformed cellular shape in treated Hep 3B were observable. Chemometric analysis revealed hydrophobic metabolites were significantly altered. Elevated vitamin D and derivatives tend to up-regulation Ca2+ and ROS subsequently triggering apoptosis. Dysregulated glycerolipids may suggest that they were biotransformed to compensate the needs of phospholipids during cell damage. Perturbation of sphingolipids, ceramide and carbohydrate-conjugated ceramides species increased the release of pro-apoptotic components reside within mitochondria and promote programmed cell death in treated Hep 3B. To conclude, MS-based metabolomics enabled the characterization of Sinularia sp. extract-induced cell death. PMID: 30587039 [PubMed - as supplied by publisher]

We Are What We Eat: A Stoichiometric and Ecometabolomic Study of Caterpillars Feeding on Two Pine Subspecies of Pinus sylvestris.

Fri, 28/12/2018 - 12:43
Related Articles We Are What We Eat: A Stoichiometric and Ecometabolomic Study of Caterpillars Feeding on Two Pine Subspecies of Pinus sylvestris. Int J Mol Sci. 2018 Dec 24;20(1): Authors: Rivas-Ubach A, Peñuelas J, Hódar JA, Oravec M, Paša-Tolić L, Urban O, Sardans J Abstract Many studies have addressed several plant-insect interaction topics at nutritional, molecular, physiological, and evolutionary levels. However, it is still unknown how flexible the metabolism and the nutritional content of specialist insect herbivores feeding on different closely related plants can be. We performed elemental, stoichiometric, and metabolomics analyses on leaves of two coexisting Pinus sylvestris subspecies and on their main insect herbivore; the caterpillar of the processionary moth (Thaumetopoea pityocampa). Caterpillars feeding on different pine subspecies had distinct overall metabolome structure, accounting for over 10% of the total variability. Although plants and insects have very divergent metabolomes, caterpillars showed certain resemblance to their plant-host metabolome. In addition, few plant-related secondary metabolites were found accumulated in caterpillar tissues which could potentially be used for self-defense. Caterpillars feeding on N and P richer needles had lower N and P tissue concentration and higher C:N and C:P ratios, suggesting that nutrient transfer is not necessarily linear through trophic levels and other plant-metabolic factors could be interfering. This exploratory study showed that little chemical differences between plant food sources can impact the overall metabolome of specialist insect herbivores. Significant nutritional shifts in herbivore tissues could lead to larger changes of the trophic web structure. PMID: 30586850 [PubMed - in process]

A Glycolytic Switch is Required for Transdifferentiation to Endothelial Lineage.

Fri, 28/12/2018 - 12:43
Related Articles A Glycolytic Switch is Required for Transdifferentiation to Endothelial Lineage. Circulation. 2018 Sep 28;: Authors: Lai L, Reineke E, Hamilton DJ, Cooke JP Abstract BACKGROUND: Previously we have shown that activation of cell-autonomous innate immune signaling facilitates the trandifferentiation of fibroblasts into induced endothelial cells (iECs), and is required to generate iECs with high fidelity for endothelial lineage. Recent studies indicate that a glycolytic switch plays a role in iPSC generation from somatic cells. METHODS: Seahorse and metabolomics flux assays were used to measure the metabolic changes during transdifferentiation in vitro, and matrigel plug assay was used to assess the effects of glycolysis modulators on transdifferentiation in vivo. RESULTS: The metabolic switch begins rapidly after activation of innate immunity, prior to the expression of markers of endothelial lineage. Inhibiting glycolysis impaired, whereas facilitating glycolysis enhanced, the generation of iECs. The TLR3 agonist PolyI:C increased expression of the mitochondrial citrate transporter Slc25A1, and the nuclear ATP-citrate lyase(ACL), in association with intracellular accumulation of citrate, the precursor for acetyl-CoA. These metabolic changes were coordinated with increased histone acetylation during transdifferentiation. CONCLUSIONS: Innate immune signaling promotes a glycolytic switch that is required for transdifferentiation, both processes being attenuated by ACL knockdown. These data shed light on a novel link between metabolism and epigenetic modulation in transdifferentiation. PMID: 30586707 [PubMed - as supplied by publisher]

Transient Nutrient Deprivation Promotes Macropinocytosis-Dependent Intracellular Bacterial Community Development.

Fri, 28/12/2018 - 12:43
Related Articles Transient Nutrient Deprivation Promotes Macropinocytosis-Dependent Intracellular Bacterial Community Development. mSphere. 2018 09 12;3(5): Authors: Hardison RL, Heimlich DR, Harrison A, Beatty WL, Rains S, Moseley MA, Thompson JW, Justice SS, Mason KM Abstract Nutrient limitation restricts bacterial growth in privileged sites such as the middle ear. Transient heme-iron restriction of nontypeable Haemophilus influenzae (NTHI), the major causative agent of chronic and recurrent otitis media (OM), promotes new and diverse phenotypes that can influence planktonic, biofilm, and intracellular lifestyles of NTHI. However, the bacterial responses to nutrient restriction that impact intracellular fate and survival of NTHI are unknown. In this work, we provide evidence for the role of transient heme-iron restriction in promoting the formation of intracellular bacterial communities (IBCs) of NTHI both in vitro and in vivo in a preclinical model of OM. We show that transient heme-iron restriction of NTHI results in significantly increased invasion and intracellular populations that escape or evade the endolysosomal pathway for increased intracellular survival. In contrast, NTHI continuously exposed to heme-iron traffics through the endolysosomal pathway for degradation. The use of pharmacological inhibitors revealed that prior heme-iron status does not appear to influence NTHI internalization through endocytic pathways. However, inhibition of macropinocytosis altered the intracellular fate of transiently restricted NTHI for degradation in the endolysosomal pathway. Furthermore, prevention of macropinocytosis significantly reduced the number of IBCs in cultured middle ear epithelial cells, providing evidence for the feasibility of this approach to reduce OM persistence. These results reveal that microenvironmental cues can influence the intracellular fate of NTHI, leading to new mechanisms for survival during disease progression.IMPORTANCE Otitis media is the most common bacterial infection in childhood. Current therapies are limited in the prevention of chronic or recurrent otitis media which leads to increased antibiotic exposure and represents a significant socioeconomic burden. In this study, we delineate the effect of nutritional limitation on the intracellular trafficking pathways used by nontypeable Haemophilus influenzae (NTHI). Moreover, transient limitation of heme-iron led to the development of intracellular bacterial communities that are known to contribute to persistence and recurrence in other diseases. New approaches for therapeutic interventions that reduce the production of intracellular bacterial communities and promote trafficking through the endolysosomal pathway were revealed through the use of pharmacological inhibition of macropinocytosis. This work demonstrates the importance of an intracellular niche for NTHI and provides new approaches for intervention for acute, chronic, and recurring episodes of otitis media. PMID: 30209128 [PubMed - indexed for MEDLINE]

Lipidomic profiling reveals early-stage metabolic dysfunction in overweight or obese humans.

Thu, 27/12/2018 - 12:05
Lipidomic profiling reveals early-stage metabolic dysfunction in overweight or obese humans. Biochim Biophys Acta Mol Cell Biol Lipids. 2018 Dec 23;: Authors: Mousa A, Naderpoor N, Mellett N, Wilson K, Plebanski M, Meikle PJ, de Courten B Abstract BACKGROUND: Advances in mass spectrometry and lipidomics techniques are providing new insights into the role of lipid metabolism in obesity-related diseases. However, human lipidomic studies have been inconsistent, owing to the use of indirect proxy measures of metabolic outcomes and relatively limited coverage of the lipidome. Here, we employed comprehensive lipid profiling and gold-standard metabolic measures to test the hypothesis that distinct lipid signatures in obesity may signify early stages of pathogenesis toward type 2 diabetes. METHODS: Using high-performance liquid chromatography-electrospray tandem mass spectrometry, we profiled >450 lipid species across 26 classes in 65 overweight or obese non-diabetic individuals. Intensive metabolic testing was conducted using direct gold-standard measures of adiposity (% body fat by dual X-ray absorptiometry), insulin sensitivity (hyperinsulinaemic-euglycaemic clamps), and insulin secretion (intravenous glucose tolerance tests), as well as measurement of serum inflammatory cytokines and adipokines (multiplex assays; flow cytometry). Univariable and multivariable linear regression models were computed using Matlab R2011a, and all analyses were corrected for multiple testing using the Benjamini-Hochberg method. RESULTS: We present new evidence showing a strong and independent positive correlation between the lysophosphatidylinositol (LPI) lipid class and insulin secretion in vivo in humans (β [95% CI] = 781.9 [353.3, 1210.4], p = 0.01), supporting the insulinotropic effects of LPI demonstrated in mouse islets. Dihydroceramide, a sphingolipid precursor, was independently and negatively correlated with insulin sensitivity (β [95% CI] = -1.9 [-2.9, -0.9], p = 0.01), indicating a possible upregulation in sphingolipid synthesis in obese individuals. These associations remained significant in multivariable models adjusted for age, sex, and % body fat. The dihexosylceramide class correlated positively with interleukin-10 before and after adjustment for age, sex, and % body fat (p = 0.02), while the phosphatidylethanolamine class and its vinyl ether-linked (plasmalogen) derivatives correlated negatively with % body fat in both univariable and age- and sex-adjusted models (all p < 0.04). CONCLUSIONS: Our data suggest that these lipid classes may signify early pathogenesis toward type 2 diabetes and could serve as novel therapeutic targets or biomarkers for diabetes prevention. PMID: 30586632 [PubMed - as supplied by publisher]

Peak annotation and verification engine (PAVE) for untargeted LC-MS metabolomics.

Thu, 27/12/2018 - 12:05
Peak annotation and verification engine (PAVE) for untargeted LC-MS metabolomics. Anal Chem. 2018 Dec 26;: Authors: Wang L, Xing X, Chen L, Yang L, Su X, Rabitz HA, Lu W, Rabinowitz JD Abstract Untargeted metabolomics can detect more than 10,000 peaks in a single LC-MS run. The correspondence between these peaks and metabolites, however, remains unclear. Here we introduce a Peak Annotation and Verification Engine (PAVE) for systematically annotating untargeted microbial metabolomics data. The workflow involves growing cells in 13C and 15N isotope-labeled media to identify peaks from biological compounds and their carbon and nitrogen atom counts. Improved de-isotoping and de-adducting is enabled by algorithms that integrate positive mode, negative mode and labeling data. To distinguish metabolites and their fragments, PAVE experimentally measures the response of each peak to a weak in-source collision-induced-dissociation voltage, which increases the peak intensity for fragments while decreasing it for their parent ions. The molecular formulae of the putative metabolites are then assigned based on database searching using both m/z and C/N atom counts. Application of this procedure to S. cerevisiae and E. coli revealed that more than 80% peaks do not label, i.e. are environmental contaminants. More than 70% of the biological peaks are isotopic variants, adducts, fragments, or mass spectrometry artifacts yielding ~2,000 apparent metabolites across the two organisms. About 650 match to a known metabolite formula based on m/z and C/N atom counts, with 220 assigned structures based on MS/MS and/or retention time to match to authenticated standards. Thus, PAVE provides an efficient route to systematically annotate LC-MS metabolomics data. PMID: 30586294 [PubMed - as supplied by publisher]

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