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: 32 min 8 sec ago

Metabolic dynamics and physiological adaptation of Panax ginseng during development.

Sun, 19/11/2017 - 13:01
Related Articles Metabolic dynamics and physiological adaptation of Panax ginseng during development. Plant Cell Rep. 2017 Nov 17;: Authors: Kim YJ, Joo SC, Shi J, Hu C, Quan S, Hu J, Sukweenadhi J, Mohanan P, Yang DC, Zhang D Abstract KEY MESSAGE: The dynamics of metabolites from leaves to roots of Panax ginseng during development has revealed the tissue-specific and year-specific metabolic networks. Being an essential Oriental medicinal plant, ginseng (Panax ginseng Meyer) is a slow-growing perennial herb-accumulating pharmaceutically active metabolites such as ginsenosides in roots during growth. However, little is known about how ginseng plants survive in the harsh environments such as winter cold and summer heat for a longer period and accumulates those active metabolites as the plant grows. To understand the metabolic kinetics in both source and sink organs such as leaves and roots of ginseng plant, respectively, and to assess the changes in ginsenosides biosynthesis during ginseng growth, we investigated the metabolic profiles from leaves and roots of 1-, 4-, and 6-year-old field-grown ginseng plants. Using an integrated non-targeted metabolomic approach, we identified in total 348 primary and secondary metabolites, which provided us for the first time a global metabolomic assessment of ginseng during growth, and morphogenesis. Strikingly, the osmoprotectants and oxidized chemicals were highly accumulated in 4- and 6-year-old ginseng leaves suggested that ginseng develop a wide range of metabolic strategies to adapt unfavorable conditions as they mature. In 6-year-old plants, ginsenosides were decreased in leaves but increased in roots up to 1.2- to sixfold, supporting the view that there is a long-distance transport of ginsenosides from leaves to roots as ginseng plants mature. Our findings provide insights into the metabolic kinetics during the development of ginseng plant and this could complement the pharmacological importance of ginseng and its compounds according to their age. PMID: 29150823 [PubMed - as supplied by publisher]

NMR Metabolomics for Stem Cell type discrimination.

Sun, 19/11/2017 - 13:01
Related Articles NMR Metabolomics for Stem Cell type discrimination. Sci Rep. 2017 Nov 17;7(1):15808 Authors: Castiglione F, Ferro M, Mavroudakis E, Pellitteri R, Bossolasco P, Zaccheo D, Morbidelli M, Silani V, Mele A, Moscatelli D, Cova L Abstract Cell metabolism is a key determinant factor for the pluripotency and fate commitment of Stem Cells (SCs) during development, ageing, pathological onset and progression. We derived and cultured selected subpopulations of rodent fetal, postnatal, adult Neural SCs (NSCs) and postnatal glial progenitors, Olfactory Ensheathing Cells (OECs), respectively from the subventricular zone (SVZ) and the olfactory bulb (OB). Cell lysates were analyzed by proton Nuclear Magnetic Resonance ((1)H-NMR) spectroscopy leading to metabolites identification and quantitation. Subsequent multivariate analysis of NMR data by Principal Component Analysis (PCA), and Partial Least Square Discriminant Analysis (PLS-DA) allowed data reduction and cluster analysis. This strategy ensures the definition of specific features in the metabolic content of phenotypically similar SCs sharing a common developmental origin. The metabolic fingerprints for selective metabolites or for the whole spectra demonstrated enhanced peculiarities among cell types. The key result of our work is a neat divergence between OECs and the remaining NSC cells. We also show that statistically significant differences for selective metabolites characterizes NSCs of different ages. Finally, the retrived metabolome in cell cultures correlates to the physiological SC features, thus allowing an integrated bioengineering approach for biologic fingerprints able to dissect the (neural) SC molecular specificities. PMID: 29150616 [PubMed - in process]

Mitochondrial DNA changes in pedunculopontine cholinergic neurons in Parkinson's.

Sat, 18/11/2017 - 12:27
Mitochondrial DNA changes in pedunculopontine cholinergic neurons in Parkinson's. Ann Neurol. 2017 Nov 17;: Authors: Bury AG, Pyle A, Elson JL, Greaves L, Morris CM, Hudson G, Pienaar IS Abstract In Parkinson's disease (PD), mitochondrial dysfunction associates with nigral dopaminergic neuronal loss. Cholinergic neuronal loss co-occurs, particularly within a brainstem structure, the pedunculopontine nucleus (PPN). We isolated single cholinergic neurons from post-mortem PPNs of aged controls and PD patients. Mitochondrial DNA (mtDNA) copy number and mtDNA deletions were increased significantly in PD patients compared to controls. Furthermore, compared to controls the PD patients had significantly more PPN cholinergic neurons containing mtDNA deletion levels exceeding 60%, a level associated with deleterious effects on oxidative phosphorylation. The current results differ from studies reporting mtDNA depletion in nigral dopaminergic neurons of PD patients. This article is protected by copyright. All rights reserved. PMID: 29149768 [PubMed - as supplied by publisher]

Effects of Tao-Hong-Si-Wu decoction on acute blood stasis in rats based on a LC-Q/TOF-MS metabolomics and network approach.

Sat, 18/11/2017 - 12:27
Effects of Tao-Hong-Si-Wu decoction on acute blood stasis in rats based on a LC-Q/TOF-MS metabolomics and network approach. Biomed Chromatogr. 2017 Nov 17;: Authors: Ma Q, Li PL, Hua YL, Ji P, Yao WL, Zhang XS, Zhong LJ, Wei YM Abstract A novel approach using metabolomics coupled with a metabolic network was used to investigate the effects of THSWD on the rat model of acute blood stasis syndrome. Acute blood stasis syndrome was induced by placing the rats in ice-cold water following two injections with epinephrine. The hemorheological indicators (WBV and PV), and the blood coagulation indicators (TT, PT, APTT, and FIB) were detected. The nonparametric univariate method and multivariate statistical analysis were performed for determining the potential biomarkers. A correlation map was structured between biochemical indicators and hub metabolites to explain the effects mechanism of THSWD. After the administration of THSWD, the levels of WBV, PV, TT, APTT, and FIB returned to levels observed in the control group. According to metabolomics coupled with metabolic network analysis, the intervention of THSWD in rats with acute blood stasis syndrome induced substantial and characteristic changes in their metabolic profiles. Fifteen metabolites were screened, which mainly involved ten pathways and five hub metabolites, namely, L-glutamate, L-phenylalanine, N-acylsphingosine, arachidonic acid and phosphatidate. The biochemical indicators and hub metabolites could be adjusted close to normal levels by THSWD. Therefore, combining metabolomics and metabolic network helped evaluate the effects of THSWD on acute blood stasis. PMID: 29149492 [PubMed - as supplied by publisher]

Evolution of the metabolome in response to selection for increased immunity in populations of Drosophila melanogaster.

Sat, 18/11/2017 - 12:27
Evolution of the metabolome in response to selection for increased immunity in populations of Drosophila melanogaster. PLoS One. 2017;12(11):e0188089 Authors: Gogna N, Sharma R, Gupta V, Dorai K, Prasad NG Abstract We used NMR-based metabolomics to test two hypotheses-(i) there will be evolved differences in the metabolome of selected and control populations even under un-infected conditions and (ii) post infection, the metabolomes of the selected and control populations will respond differently. We selected replicate populations of Drosophila melanogaster for increased survivorship (I) against a gram-negative pathogen. We subjected the selected (I) and their control populations (S) to three different treatments: (1) infected with heat-killed bacteria (i), (2) sham infected (s), and (3) untreated (u). We performed 1D and 2D NMR experiments to identify the metabolic differences. Multivariate analysis of the metabolic profiles of the untreated (Iu and Su) flies yielded higher concentrations of lipids, organic acids, sugars, amino acids, NAD and AMP in the Iu treatment as compared to the Su treatment, showing that even in the absence of infection, the metabolome of the I and S regimes was different. In the S and I regimes, post infection/injury, concentration of metabolites directly or indirectly associated with energy related pathways (lipids, organic acids, sugars) declined while the concentration of metabolites that are probably associated with immune response (amino acids) increased. However, in most cases, the I regime flies had a higher concentration of such metabolites even under un-infected conditions. The change in the metabolite concentration upon infection/injury was not always comparable between I and S regimes (in case of lactate, alanine, leucine, lysine, threonine) indicating that the I and S regimes had evolved to respond differentially to infection and to injury. PMID: 29149207 [PubMed - in process]

Proton Nuclear Magnetic Resonance (¹H-NMR)-Based Metabolomic Evaluation of Human Renal Allografts from Donations After Circulatory Death.

Sat, 18/11/2017 - 12:27
Proton Nuclear Magnetic Resonance (¹H-NMR)-Based Metabolomic Evaluation of Human Renal Allografts from Donations After Circulatory Death. Med Sci Monit. 2017 Nov 17;23:5472-5479 Authors: Wang Z, Yang H, Zhao C, Wei J, Wang J, Han Z, Tao J, Xu Z, Ju X, Tan R, Gu M Abstract BACKGROUND Delayed graft function (DGF) is a common complication that impairs allograft function after kidney transplantation. However, the mechanism of DGF remains unclear. Nuclear magnetic resonance (NMR)-based analysis has been widely used in recent times to assess changes in metabolite levels. MATERIAL AND METHODS Samples of perfusate from allografts donated after circulatory death were collected prior to transplantation, during static cold storage. ¹H-NMR-based metabolomics combined with the statistical methods, orthogonal partial least-squares discriminant analysis (OPLS-DA), and principle-component analysis (PCA), were employed to test different levels of metabolites between the allografts that exhibited DGF and those that exhibited immediate graft function (IGF). RESULTS The study population consisted of 36 subjects, 11 with DGF and 25 with IGF. Of the 37 detected and identified metabolites, a-glucose and citrate were significantly elevated in the perfusate of DGF allografts, and taurine and betaine were significantly decreased. CONCLUSIONS ¹H-NMR analysis of DGF and IGF perfusates revealed some significant differences in their metabolite profiles, which may help explain the mechanisms of kidney ischemia-reperfusion injury and DGF. PMID: 29149095 [PubMed - in process]

Themed issue on 'emerging technologies in mass spectrometry'.

Sat, 18/11/2017 - 12:27
Themed issue on 'emerging technologies in mass spectrometry'. Bioanalysis. 2017 Nov;9(21):1617-1618 Authors: Campbell JL, Plumb R PMID: 29148832 [PubMed - in process]

Metabolic effects of p,p'-DDE on Atlantic salmon hepatocytes.

Sat, 18/11/2017 - 12:27
Metabolic effects of p,p'-DDE on Atlantic salmon hepatocytes. J Appl Toxicol. 2017 Nov 17;: Authors: Olsvik PA, Søfteland L Abstract Decades after being banned in many countries, DDT and its metabolites are still considered major environmental hazards. The p,p'-DDE isomer, the DDT metabolite found in highest concentration in aquaculture feeds, is an endocrine disruptor with demonstrated ability to induce epigenetic effects. This study aimed at examining the impact of p,p'-DDE on Atlantic salmon. Primary hepatocytes were exposed to four concentrations of p,p'-DDE (0.1, 1, 10, 100 μm) for 48 hours, and endpoints included cytotoxicity, global DNA methylation, targeted transcription and metabolomics profiling (100 μm). p,p'-DDE was moderately cytotoxic at 100 μm. No impact was seen on global DNA methylation. Vtg1 and esr1 transcription, markers of endocrine disruption, was most strongly induced at 10 μm p,p'-DDE, while ar showed strongest response at 100 μm. Metabolomics profiling showed that p,p'-DDE at 100 μm most strongly affected carbohydrate metabolism, primary bile acid metabolism, leucine, isoleucine and valine metabolism, diacylglycerol and sphingolipid metabolism. Observed changes in lipid levels suggest that p,p'-DDE interferes with phospholipid membrane biosynthesis. Elevation of bile acid levels in p,p'-DDE-exposed hepatocytes indicates upregulation of synthesis of bile acids after cytochrome P450 activation. Pathway analysis showed that the superpathway of methionine degradation was the most significantly affected pathway by p,p'-DDE exposure, while endocrine system disorder topped the diseases and disorder ranking. In conclusion, this work predicts an endocrine response to p,p'-DDE exposure, and demonstrates how this legacy pesticide might interfere with mechanisms linked to DNA methylation in Atlantic salmon hepatocytes. PMID: 29148584 [PubMed - as supplied by publisher]

Trial watch: Immune checkpoint blockers for cancer therapy.

Sat, 18/11/2017 - 12:27
Trial watch: Immune checkpoint blockers for cancer therapy. Oncoimmunology. 2017;6(11):e1373237 Authors: Vanpouille-Box C, Lhuillier C, Bezu L, Aranda F, Yamazaki T, Kepp O, Fucikova J, Spisek R, Demaria S, Formenti SC, Zitvogel L, Kroemer G, Galluzzi L Abstract Immune checkpoint blockers (ICBs) are literally revolutionizing the clinical management of an ever more diversified panel of oncological indications. Although considerable attention persists around the inhibition of cytotoxic T lymphocyte-associated protein 4 (CTLA4) and programmed cell death 1 (PDCD1, best known as PD-1) signaling, several other co-inhibitory T-cell receptors are being evaluated as potential targets for the development of novel ICBs. Moreover, substantial efforts are being devoted to the identification of biomarkers that reliably predict the likelihood of each patient to obtain clinical benefits from ICBs in the absence of severe toxicity. Tailoring the delivery of specific ICBs or combinations thereof to selected patient populations in the context of precision medicine programs constitutes indeed a major objective of the future of ICB-based immunotherapy. Here, we discuss recent preclinical and clinical advances on the development of ICBs for oncological indications. PMID: 29147629 [PubMed]

Trial Watch: Adoptively transferred cells for anticancer immunotherapy.

Sat, 18/11/2017 - 12:27
Trial Watch: Adoptively transferred cells for anticancer immunotherapy. Oncoimmunology. 2017;6(11):e1363139 Authors: Fournier C, Martin F, Zitvogel L, Kroemer G, Galluzzi L, Apetoh L Abstract Immunotherapies aimed at strengthening immune effector responses against malignant cells are growing at exponential rates. Alongside, the impressive benefits obtained by patients with advanced melanoma who received adoptively transferred tumor-infiltrating lymphocytes (TILs) have encouraged the scientific community to pursue adoptive cell transfer (ACT)-based immunotherapy. ACT involves autologous or allogenic effector lymphocytes that are generally obtained from the peripheral blood or resected tumors, expanded and activated ex vivo, and administered to lymphodepleted patients. ACT may be optionally associated with chemo- and/or immunotherapeutics, with the overall aim of enhancing the proliferation, persistence and functionality of infused cells, as well as to ensure their evolution in an immunological permissive local and systemic microenvironment. In addition, isolated lymphocytes can be genetically engineered to endow them with the ability to target a specific tumor-associated antigen (TAA), to increase their lifespan, and/or to reduce their potential toxicity. The infusion of chimeric antigen receptor (CAR)-expressing cytotoxic T lymphocytes redirected against CD19 has shown promising clinical efficacy in patients with B-cell malignancies. Accordingly, the US Food and Drug Administration (FDA) has recently granted 'breakthrough therapy' designation to a CAR-based T-cell therapy (CTL019) for patients with B-cell malignancies. Considerable efforts are now being devoted to the development of efficient ACT-based immunotherapies for non-hematological neoplasms. In this Trial Watch, we summarize recent clinical advances on the use of ACT for oncological indications. PMID: 29147628 [PubMed]

Depletion of Stercobilin in Fecal Matter from a Mouse Model of Autism Spectrum Disorders.

Sat, 18/11/2017 - 12:27
Depletion of Stercobilin in Fecal Matter from a Mouse Model of Autism Spectrum Disorders. Metabolomics. 2017 Nov;13(11): Authors: Sekera ER, Rudolph HL, Carro SD, Morales MJ, Bett GCL, Rasmusson RL, Wood TD Abstract Introduction: Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders lacking a clinical biomarker for diagnosis. Emerging evidence shows that intestinal microflora from ASD subjects can be distinguished from controls, suggesting metabolite differences due to the action of intestinal microbes may provide a means for identifying potential biomarkers for ASD. Objectives: The aim of this study was to determine if quantitative differences in levels of stercobilin and stercobilinogen, metabolites produced by biological action of intestinal microflora, exist in the fecal matter between an ASD mouse model population and controls. Methods: Pairs of fecal samples were collected from two mouse groups, an ASD model group with Timothy syndrome 2 (TS2-NEO) and a gender-matched control group. After centrifugation, supernatant was spiked with an (18)O-labeled stercobilin isotopomer and subjected to solid phase extraction for processing. Extracted samples were spotted on a stainless steel plate and subjected to matrix-assisted laser desorption and ionization mass spectrometry using dihydroxybenzoic acid as the matrix (n = 5). Peak areas for bilins and (18)O-stercobilin isotopomers were determined in each fecal sample. Results: A 40-45% depletion in stercobilin in TS2-NEO fecal samples compared with controls was observed with p < 0.05; a less dramatic depletion was observed for stercobilinogen. Conclusions: The results show that stercobilin depletion in feces is observed for an ASD mouse model vs. controls. This may help to explain recent observations of a less diverse microbiome in humans with ASD and may prove helpful in developing a clinical ASD biomarker. PMID: 29147105 [PubMed]

Disturbance in Plasma Metabolic Profile in Different Types of Human Cytomegalovirus-Induced Liver Injury in Infants.

Sat, 18/11/2017 - 12:27
Disturbance in Plasma Metabolic Profile in Different Types of Human Cytomegalovirus-Induced Liver Injury in Infants. Sci Rep. 2017 Nov 16;7(1):15696 Authors: Li WW, Shan JJ, Lin LL, Xie T, He LL, Yang Y, Wang SC Abstract Human cytomegalovirus (HCMV) infection in infants is a global problem and the liver is a target organ of HCMV invasion. However, the mechanism by which HCMV causes different types of liver injury is unclear, and there are many difficulties in the differential diagnosis of HCMV infantile cholestatic hepatopathy (ICH) and extrahepatic biliary atresia (EHBA). We established a non-targeted gas chromatography-mass spectrometry metabolomics method in conjunction with orthogonal partial least squares-discriminate analysis based on 127 plasma samples from healthy controls, and patients with HCMV infantile hepatitis, HCMV ICH, and HCMV EHBA to explore the metabolite profile of different types of HCMV-induced liver injury. Twenty-nine metabolites related to multiple amino acid metabolism disorder, nitrogen metabolism and energy metabolism were identified. Carbamic acid, glutamate, L-aspartic acid, L-homoserine, and noradrenaline for HCMV ICH vs. HCMV EHBA were screened as potential biomarkers and showed excellent discriminant performance. These results not only revealed the potential pathogenesis of HCMV-induced liver injury, but also provided a feasible diagnostic tool for distinguishing EHBA from ICH. PMID: 29146975 [PubMed - in process]

Diacylglycerols as biomarkers of sustained immune activation in Proteinopathies associated with dementia.

Sat, 18/11/2017 - 12:27
Diacylglycerols as biomarkers of sustained immune activation in Proteinopathies associated with dementia. Clin Chim Acta. 2017 Nov 13;: Authors: Wood PL, Cebak JE, Woltjer RL Abstract Cognitive decline is a devastating clinical condition, heavily correlated with age progression. In the cases of Alzheimer's disease, Parkinson's disease, and Lewy body disease, the common neuropathologies are proteinopathies and neuroinflammation. Herein, we review current lipidomics findings and conclude that brain and circulating diacylglycerols represent biomarkers of this ongoing sustained immune response, presumably involving microglia. We further hypothesize that a logical next step will be to evaluate biomarkers of immune activation in a cohort of patients with Mild Cognitive Impairment (MCI) and subsequently attempt to provide therapeutic intervention with anti-inflammatory therapy in MCI patients with immune activation. Although this is an urgent and theoretically safe therapeutic trial, it will likely necessitate government support. PMID: 29146478 [PubMed - as supplied by publisher]

PHEOCHROMOCYTOMA: A GENETIC AND DIAGNOSTIC UPDATE.

Sat, 18/11/2017 - 12:27
PHEOCHROMOCYTOMA: A GENETIC AND DIAGNOSTIC UPDATE. Endocr Pract. 2017 Nov 16;: Authors: Mercado-Asis LB, Wolf KI, Jochmanova I, Taïeb D Abstract OBJECTIVE: Pheochromocytomas and paragangliomas (PPGLs) are neuroendocrine tumors derived from adrenal or extra-adrenal locations, respectively. Upon suspicion of PPGL, specific metabolomic, molecular, biochemical, imaging, and histopathological studies are performed to prove, localize, treat, and monitor disease progression. Recently, improved diagnostic tools allow physicians to accurately diagnose PPGL, even in patients presenting with small (less than 1 cm) or biochemically silent tumors, which previously delayed proper detection and treatment. METHODS: This review outlines the most updated approach to PPGL patients, and presents a new diagnostic approach for physicians in order to increase earlier tumor identification and accurately assess metastatic behavior. CONCLUSION: We present the most recent advances in genetics, epigenetics, metabolomics, biochemical, and imaging diagnoses of this rare tumor in order to properly assess disease, decide treatment options, and manage follow-up. We also elaborate on new therapeutic perspectives in these very rare neoplastic entities. ABBREVIATIONS: 177Lu-DOTATATE = lutetium octreotate; ACO = aconitase; Ad = adenine; AD = autosomal dominant; ATRX = ATRX chromatin remodeler; ccRCC = clear cell renal cell carcinoma; c-MYC = MYC proto oncognene; CoA = coenzyme A; COMT = catechol-O-methyl transferase; CPE = carboxypeptidase E; CS = citrate synthase; CT = computed tomography; DH = pyruvate dehydrogenase; DOTATATE = DOTA-octreotate; EGLN1/2 = egl-9 family hypoxia inducible factor 1/2; EGLN2/PHD1 = egl-9 family hypoxia inducible factor 2; elF-4E = eukaryotic initiation factor 4E; EMT = epithelial-to-mesenchymal transition; EPAS1/HIF2A = endothelial PAS domain protein 2/hypoxia-inducible factor 2α; ERK = extracellular signal-regulated kinase; FH = fumarate hydroxylase; GSH = glutathione; H3F3A = histone 3.3 encoding gene; HIFs = Hypoxia-inducible factors; HIF-α = hypoxia-inducible factor alpha; HNPGLs = head and neck paragangliomas; HRAS = HRas protooncogene; IDH = isocitrate dehydrogenase; IGF-1R = growth factor 1 receptor; KIF1B = kinesin family member 1B; MAX = myc-associated factor X; MDH2 = malate dehydrogenase; MN = metanephrine; MRI = magnetic resonance imaging; mTORC1 = mammalian target of rapamycin complex 1; MTY = methoxytyramine; NAd = nicotinamide adenine dinucleotide; NETs = neuroendocrine tumors; NF1 = neurofibromin 1; NMN = normetanephrine; OPLS-DA = orthogonal partial least square discriminant analysis; PFS = progression free survival; PHD = prolyl hydroxylase domain protein; PPGLs = Pheochromocytoma and Paragangliomas; PRRT = peptide receptor radionuclide therapy; Pvhl = von Hippel-Lindau protein; Raptor = regulatory associated protein of mTOR; RAS = rat sarcoma oncogene; RET = rearranged during transfection proto-oncogene; ROS = reactive oxygen species; S6K = S6 kinase; SDH = succinate dehydrogenase; SDHA, -B, -C, -D, = succinate dehydrogenase subunits A, B, C, D; SDHAF2 = succinate dehydrogenase complex assembly factor 2; SDHB, C, D = succinate dehydrogenase subunits B, C, D; SDHx = succinate dehydrogenase subunits; SSTRs = somatostatin receptors; SUCLG = succinyl-CoA synthase; TERRA = Telomeric Repeat-containing RNA; TET = ten-eleven-translocation methylcytosine dioxygenase; TMEM127 = transmembrane protein 127; VEGF = vascular endothelial growth factor; VHL = von Hippel-Lindau; α-KGDH = alpha-ketoglutarate dehydrogenase. PMID: 29144820 [PubMed - as supplied by publisher]

Metabolic profiling of normal hepatocyte and hepatocellular carcinoma cells via (1) H nuclear magnetic resonance spectroscopy.

Fri, 17/11/2017 - 15:01
Metabolic profiling of normal hepatocyte and hepatocellular carcinoma cells via (1) H nuclear magnetic resonance spectroscopy. Cell Biol Int. 2017 Nov 16;: Authors: Chen Y, Chen Z, Feng JH, Chen YB, Liao NS, Su Y, Zou CY Abstract Hepatocellular carcinoma (HCC) causes death mainly by disseminated metastasis progression from the organ being confined. Different metastatic stages are closely related to cellular metabolic profiles. Normal hepatocyte and HepG2 cell line from low metastatic HCC were studied by NMR-based metabolomic techniques. Multivariate and univariate statistical analyses were utilized to identify characteristic metabolites from cells and cultured media. Elevated levels of acetate, creatine, isoleucine, leucine, and phenylalanine were observed in HepG2 cells, suggesting more active in gathering nutrient components along with altered amino acid metabolisms and enhanced lipid metabolism. High glucose consumption was significantly different in low metastatic cells. A series of characteristic metabolites were identified and served as biomarkers. Relative metabolic pathway analysis shows that low metastatic HepG2 cell line exhibits active behaviors in metabolisms and biosynthesis of specific amino acids and energy metabolism. Moreover, characteristic metabolites-based classification models executed by support vector machines algorithm perform robustly to classify normal hepatocyte and HepG2 cell line. It is concluded that NMR-based metabolomic analyses of cell lines can provide a powerful approach to understand metastasis-related biological alterations. The present study also provides a basis for metabolic markers determination of hepatic carcinoma in the future clinical study. PMID: 29144590 [PubMed - as supplied by publisher]

A ubiquitin-dependent signalling axis specific for ALKBH-mediated DNA dealkylation repair.

Fri, 17/11/2017 - 15:01
A ubiquitin-dependent signalling axis specific for ALKBH-mediated DNA dealkylation repair. Nature. 2017 Nov 16;551(7680):389-393 Authors: Brickner JR, Soll JM, Lombardi PM, Vågbø CB, Mudge MC, Oyeniran C, Rabe R, Jackson J, Sullender ME, Blazosky E, Byrum AK, Zhao Y, Corbett MA, Gécz J, Field M, Vindigni A, Slupphaug G, Wolberger C, Mosammaparast N Abstract DNA repair is essential to prevent the cytotoxic or mutagenic effects of various types of DNA lesions, which are sensed by distinct pathways to recruit repair factors specific to the damage type. Although biochemical mechanisms for repairing several forms of genomic insults are well understood, the upstream signalling pathways that trigger repair are established for only certain types of damage, such as double-stranded breaks and interstrand crosslinks. Understanding the upstream signalling events that mediate recognition and repair of DNA alkylation damage is particularly important, since alkylation chemotherapy is one of the most widely used systemic modalities for cancer treatment and because environmental chemicals may trigger DNA alkylation. Here we demonstrate that human cells have a previously unrecognized signalling mechanism for sensing damage induced by alkylation. We find that the alkylation repair complex ASCC (activating signal cointegrator complex) relocalizes to distinct nuclear foci specifically upon exposure of cells to alkylating agents. These foci associate with alkylated nucleotides, and coincide spatially with elongating RNA polymerase II and splicing components. Proper recruitment of the repair complex requires recognition of K63-linked polyubiquitin by the CUE (coupling of ubiquitin conjugation to ER degradation) domain of the subunit ASCC2. Loss of this subunit impedes alkylation adduct repair kinetics and increases sensitivity to alkylating agents, but not other forms of DNA damage. We identify RING finger protein 113A (RNF113A) as the E3 ligase responsible for upstream ubiquitin signalling in the ASCC pathway. Cells from patients with X-linked trichothiodystrophy, which harbour a mutation in RNF113A, are defective in ASCC foci formation and are hypersensitive to alkylating agents. Together, our work reveals a previously unrecognized ubiquitin-dependent pathway induced specifically to repair alkylation damage, shedding light on the molecular mechanism of X-linked trichothiodystrophy. PMID: 29144457 [PubMed - in process]

NMR-Based Identification of Metabolites in Polar and Non-Polar Extracts of Avian Liver.

Fri, 17/11/2017 - 15:01
NMR-Based Identification of Metabolites in Polar and Non-Polar Extracts of Avian Liver. Metabolites. 2017 Nov 16;7(4): Authors: Fathi F, Brun A, Rott KH, Falco Cobra P, Tonelli M, Eghbalnia HR, Caviedes-Vidal E, Karasov WH, Markley JL Abstract Metabolites present in liver provide important clues regarding the physiological state of an organism. The aim of this work was to evaluate a protocol for high-throughput NMR-based analysis of polar and non-polar metabolites from a small quantity of liver tissue. We extracted the tissue with a methanol/chloroform/water mixture and isolated the polar metabolites from the methanol/water layer and the non-polar metabolites from the chloroform layer. Following drying, we re-solubilized the fractions for analysis with a 600 MHz NMR spectrometer equipped with a 1.7 mm cryogenic probe. In order to evaluate the feasibility of this protocol for metabolomics studies, we analyzed the metabolic profile of livers from house sparrow (Passer domesticus) nestlings raised on two different diets: livers from 10 nestlings raised on a high protein diet (HP) for 4 d and livers from 12 nestlings raised on the HP diet for 3 d and then switched to a high carbohydrate diet (HC) for 1 d. The protocol enabled the detection of 52 polar and nine non-polar metabolites in ¹H NMR spectra of the extracts. We analyzed the lipophilic metabolites by one-way ANOVA to assess statistically significant concentration differences between the two groups. The results of our studies demonstrate that the protocol described here can be exploited for high-throughput screening of small quantities of liver tissue (approx. 100 mg wet mass) obtainable from small animals. PMID: 29144418 [PubMed]

Monitoring for Response to Antineoplastic Drugs: The Potential of a Metabolomic Approach.

Fri, 17/11/2017 - 15:01
Monitoring for Response to Antineoplastic Drugs: The Potential of a Metabolomic Approach. Metabolites. 2017 Nov 16;7(4): Authors: Rattner J, Bathe OF Abstract For most cancers, chemotherapeutic options are rapidly expanding, providing the oncologist with substantial choices. Therefore, there is a growing need to select the best systemic therapy, for any individual, that effectively halts tumor progression with minimal toxicity. Having the capability to predict benefit and to anticipate toxicity would be ideal, but remains elusive at this time. An alternative approach is an adaptive approach that involves close observation for treatment response and emergence of resistance. Currently, response to systemic therapy is estimated using radiographic tests. Unfortunately, radiographic estimates of response are imperfect and radiographic signs of response can be delayed. This is particularly problematic for targeted agents, as tumor shrinkage is often not apparent with these drugs. As a result, patients are exposed to prolonged courses of toxic drugs that may ultimately be found to be ineffective. A biomarker-based adaptive strategy that involves the serial analysis of the metabolome is attractive. The metabolome changes rapidly with changes in physiology. Changes in the circulating metabolome associated with various antineoplastic agents have been described, but further work will be required to understand what changes signify clinical benefit. We present an investigative approach for the discovery and validation of metabolomic response biomarkers, which consists of serial analysis of the metabolome and linkage of changes in the metabolome to measurable therapeutic benefit. Potential pitfalls in the development of metabolomic biomarkers of response and loss of response are reviewed. PMID: 29144383 [PubMed]

Salt-responsive gut commensal modulates TH17 axis and disease.

Fri, 17/11/2017 - 15:01
Salt-responsive gut commensal modulates TH17 axis and disease. Nature. 2017 Nov 15;: Authors: Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN Abstract A Western lifestyle with high salt consumption can lead to hypertension and cardiovascular disease. High salt may additionally drive autoimmunity by inducing T helper 17 (TH17) cells, which can also contribute to hypertension. Induction of TH17 cells depends on gut microbiota; however, the effect of salt on the gut microbiome is unknown. Here we show that high salt intake affects the gut microbiome in mice, particularly by depleting Lactobacillus murinus. Consequently, treatment of mice with L. murinus prevented salt-induced aggravation of actively induced experimental autoimmune encephalomyelitis and salt-sensitive hypertension by modulating TH17 cells. In line with these findings, a moderate high-salt challenge in a pilot study in humans reduced intestinal survival of Lactobacillus spp., increased TH17 cells and increased blood pressure. Our results connect high salt intake to the gut-immune axis and highlight the gut microbiome as a potential therapeutic target to counteract salt-sensitive conditions. PMID: 29143823 [PubMed - as supplied by publisher]

Metformin Potentiates the Benefits of Dietary Restraint: A Metabolomic Study.

Fri, 17/11/2017 - 15:01
Metformin Potentiates the Benefits of Dietary Restraint: A Metabolomic Study. Int J Mol Sci. 2017 Oct 28;18(11): Authors: Riera-Borrull M, García-Heredia A, Fernández-Arroyo S, Hernández-Aguilera A, Cabré N, Cuyàs E, Luciano-Mateo F, Camps J, Menendez JA, Joven J Abstract Prevention of the metabolic consequences of a chronic energy-dense/high-fat diet (HFD) represents a public health priority. Metformin is a strong candidate to be incorporated in alternative therapeutic approaches. We used a targeted metabolomic approach to assess changes related to the multi-faceted metabolic disturbances provoked by HFD. We evaluated the protective effects of metformin and explored how pro-inflammatory and metabolic changes respond when mice rendered obese, glucose-intolerant and hyperlipidemic were switched to diet reversal with or without metformin. Mice treated with metformin and diet-reversal showed a dramatically improved protection against HFD-induced hepatic steatosis, a beneficial effect that was accompanied by a lowering of liver-infiltrating pro-inflammatory macrophages and lower release of pro-inflammatory cytokines. Metformin combined with diet reversal promoted effective weight loss along with better glucose control, lowered levels of circulating cholesterol and triglycerides, and reduced adipose tissue content. Our findings underscored the ability of metformin to target the contribution of branched chain amino acids to adipose tissue metabolism while suppressing mitochondrial-dependent biosynthesis in hepatic tissue. The relationship between adipose tissue and liver might provide clinical potential for combining metformin and dietary modifications to protect against the metabolic damage occurring upon excessive dietary fat intake. PMID: 29143783 [PubMed - in process]

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