PubMed

A robust and extendable sheath flow interface with minimal dead volume for coupling CE with ESI-MS. Talanta. 2018 Apr 01;180:376-382 Authors: Fang P, Pan JZ, Fang Q Abstract In this paper, we describe a robust sheath flow-based CE-MS interface with minimal interface dead volume based on an extended pattern. A 20µm i.d. × 90µm o.d. fused-silica capillary with a chemically-etched thin-wall tip (30µm o.d.) was used as the separation capillary as well as electrospray emitter, and a 200µm i.d. × 375µm o.d. capillary with a tapered tip (40µm o.d.) was used as the sheath flow capillary. An extendable sheath-flow interface mode was adopted by decreasing the thickness of separation capillary tip and extending the separation capillary tip out from the sheath flow capillary tip, and allowing the sheath flow to be transferred to the separation capillary tip along its outer surface, forming a surface sheath flow to mix with sample flow at the separation capillary tip. Such a strategy could significantly reduce the interface dead volume and thus improve the CE separation efficiency and detection sensitivity, as well as evidently enhance the working reliability of the CE-MS interface. We investigated various factors affecting the interface performance, including capillary extending distance, emitter diameters, sheath flow capillary shape, and sheath flow rate. Under the optimized conditions, a minimal interface dead volume of ca. 4pL was obtained which is the smallest one compared with previously-reported sheath flow-based CE-MS interfaces. The feasibility and applicability of the present CE-MS interface were demonstrated in the separation of a peptide mixture with high separation efficiency of 2.07-3.38µm plate heights and good repeatabilities (< 6.1% RSD, n = 5). We except such a simple and robust interface could provide a possible solution for the development of commercial CE-MS interfaces differing from the currently-used ones, and has the potentials to be applied in routine analytical laboratories for various studies such as proteomics, metabolomics, or single cell analysis. PMID: 29332826 [PubMed - in process]

Salivary metabolomics profile of patients with recurrent aphthous ulcer as revealed by liquid chromatography-tandem mass spectrometry. J Int Med Res. 2018 Jan 01;:300060517745388 Authors: Li Y, Wang D, Zeng C, Liu Y, Huang G, Mei Z Abstract Objective We compared the salivary nontargeted metabolite profiles between patients with recurrent aphthous ulcer (RAU) and healthy individuals to investigate the metabolic alterations associated with RAU. Methods Saliva samples were collected from 45 patients with RAU and 49 healthy individuals, and the salivary metabolites were quantified using liquid chromatography-tandem mass spectrometry. The metabolomic profiles were then analyzed using multivariate and univariate statistical methods, and enrichment of the metabolites in various biological pathways was assessed. Results In total, 206 significant differentiating metabolites (Wilcoxon test, false discovery rate [FDR] of <0.05) were identified between patients with RAU and healthy individuals. These metabolites were implicated in tryptophan metabolism, steroid hormone biosynthesis, and other metabolic pathways. Two commonly circulating steroids, estrone sulfate and dehydroepiandrosterone sulfate, were significantly lower in the saliva of patients with RAU (Wilcoxon test, FDR < 0.05, power > 0.9). Principal component analysis and partial least-squares discriminant analysis revealed metabolic perturbations involving RAU, and receiver operating characteristic curve analysis with several metabolites showed good diagnostic ability for RAU. Conclusions The results of this study indicate that patients with RAU are characterized by metabolic imbalances. Psychogenic factors, endocrinopathies, and immunosuppression may contribute to the onset of RAU. PMID: 29332424 [PubMed - as supplied by publisher]

Related Articles Highly Time-Resolved Metabolic Reprogramming toward Differential Levels of Phosphate in Chlamydomonas reinhardtii. J Microbiol Biotechnol. 2017 Jun 28;27(6):1150-1156 Authors: Jang CH, Lee G, Park YC, Kim KH, Lee DY Abstract Understanding phosphorus metabolism in photosynthetic organisms is important as it is closely associated with enhanced crop productivity and pollution management for natural ecosystems (e.g., algal blooming). Accordingly, we exploited highly time-resolved metabolic responses to different levels of phosphate deprivation in Chlamydomonas reinhardtii, a photosynthetic model organism. We conducted non-targeted primary metabolite profiling using gas-chromatography time-of-flight mass spectrometric analysis. Primarily, we systematically identified main contributors to degree-wise responses corresponding to the levels of phosphate deprivation. Additionally, we systematically characterized the metabolite sets specific to different phosphate conditions and their interactions with culture time. Among them were various types of fatty acids that were most dynamically modulated by the phosphate availability and culture time in addition to phosphorylated compounds. PMID: 28372038 [PubMed - indexed for MEDLINE]

Related Articles Molecular Identification, Enzyme Assay, and Metabolic Profiling of Trichoderma spp. J Microbiol Biotechnol. 2017 Jun 28;27(6):1157-1162 Authors: Bae SJ, Park YH, Bae HJ, Jeon J, Bae H Abstract The goal of this study was to identify and characterize selected Trichoderma isolates by metabolic profiling and enzyme assay for evaluation of their potential as biocontrol agents against plant pathogens. Trichoderma isolates were obtained from the Rural Development Administration Genebank Information Center (Wanju, Republic of Korea). Eleven Trichoderma isolates were re-identified using ribosomal DNA internal transcribed spacer (ITS) regions. ITS sequence results showed new identification of Trichoderma isolates. In addition, metabolic profiling of the ethyl acetate extracts of the liquid cultures of five Trichoderma isolates that showed the best anti-Phytophthora activities was conducted using gas chromatography-mass spectrometry. Metabolic profiling revealed that Trichoderma isolates shared common metabolites with well-known antifungal activities. Enzyme assays indicated strong cell walldegrading enzyme activities of Trichoderma isolates. Overall, our results indicated that the selected Trichoderma isolates have great potential for use as biocontrol agents against plant pathogens. PMID: 28372034 [PubMed - indexed for MEDLINE]

Related Articles Transcriptomic and metabolic analyses provide new insights into chilling injury in peach fruit. Plant Cell Environ. 2017 Aug;40(8):1531-1551 Authors: Wang K, Yin XR, Zhang B, Grierson D, Xu CJ, Chen KS Abstract Low temperature conditioning (LTC) alleviates peach fruit chilling injury but the underlying molecular basis is poorly understood. Here, changes in transcriptome, ethylene production, flesh softening, internal browning and membrane lipids were compared in fruit maintained in constant 0 °C and LTC (pre-storage at 8 °C for 5 d before storage at 0 °C). Low temperature conditioning resulted in a higher rate of ethylene production and a more rapid flesh softening as a result of higher expression of ethylene biosynthetic genes and a series of cell wall hydrolases. Reduced internal browning of fruit was observed in LTC, with lower transcript levels of polyphenol oxidase and peroxidase, but higher lipoxygenase. Low temperature conditioning fruit also showed enhanced fatty acid content, increased desaturation, higher levels of phospholipids and a preferential biosynthesis of glucosylceramide. Genes encoding cell wall hydrolases and lipid metabolism enzymes were coexpressed with differentially expressed ethylene response factors (ERFs) and contained ERF binding elements in their promoters. In conclusion, LTC is a special case of cold acclimation which increases ethylene production and, operating through ERFs, promotes both softening and changes in lipid composition and desaturation, which may modulate membrane stability, reducing browning and contributing to alleviation of peach fruit chilling injury. PMID: 28337785 [PubMed - indexed for MEDLINE]

Related Articles Global Functional Analysis of Butanol-Sensitive Escherichia coli and Its Evolved Butanol-Tolerant Strain. J Microbiol Biotechnol. 2017 Jun 28;27(6):1171-1179 Authors: Jeong H, Lee SW, Kim SH, Kim EY, Kim S, Yoon SH Abstract Butanol is a promising alternative to ethanol and is desirable for use in transportation fuels and additives to gasoline and diesel fuels. Microbial production of butanol is challenging primarily because of its toxicity and low titer of production. Herein, we compared the transcriptome and phenome of wild-type Escherichia coli and its butanol-tolerant evolved strain to understand the global cellular physiology and metabolism responsible for butanol tolerance. When the ancestral butanol-sensitive E. coli was exposed to butanol, gene activities involved in respiratory mechanisms and oxidative stress were highly perturbed. Intriguingly, the evolved butanol-tolerant strain behaved similarly in both the absence and presence of butanol. Among the mutations occurring in the evolved strain, cis-regulatory mutations may be the cause of butanol tolerance. This study provides a foundation for the rational design of the metabolic and regulatory pathways for enhanced biofuel production. PMID: 28335589 [PubMed - indexed for MEDLINE]

Related Articles Unravelling early events in the Taphrina deformans-Prunus persica interaction: an insight into the differential responses in resistant and susceptible genotypes. Plant Cell Environ. 2017 Aug;40(8):1456-1473 Authors: Svetaz LA, Bustamante CA, Goldy C, Rivero N, Müller GL, Valentini GH, Fernie AR, Drincovich MF, Lara MV Abstract Leaf peach curl is a devastating disease affecting leaves, flowers and fruits, caused by the dimorphic fungus Taphrina deformans. To gain insight into the mechanisms of fungus pathogenesis and plant responses, leaves of a resistant and two susceptible Prunus persica genotypes were inoculated with blastospores (yeast), and the infection was monitored during 120 h post inoculation (h.p.i.). Fungal dimorphism to the filamentous form and induction of reactive oxygen species (ROS), callose synthesis, cell death and defence compound production were observed independently of the genotype. Fungal load significantly decreased after 120 h.p.i. in the resistant genotype, while the pathogen tended to grow in the susceptible genotypes. Metabolic profiling revealed a biphasic re-programming of plant tissue in susceptible genotypes, with an initial stage co-incident with the yeast form of the fungus and a second when the hypha is developed. Transcriptional analysis of PRs and plant hormone-related genes indicated that pathogenesis-related (PR) proteins are involved in P. persica defence responses against T. deformans and that salicylic acid is induced in the resistant genotype. Conducted experiments allowed the elucidation of common and differential responses in susceptible versus resistant genotypes and thus allow us to construct a picture of early events during T. deformans infection. PMID: 28244594 [PubMed - indexed for MEDLINE]

Reprogramming the metabolome rescues retinal degeneration. Cell Mol Life Sci. 2018 Jan 13;: Authors: Park KS, Xu CL, Cui X, Tsang SH Abstract Metabolomics studies in the context of ophthalmology have largely focused on identifying metabolite concentrations that characterize specific retinal diseases. Studies involving mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy have shown that individuals suffering from retinal diseases exhibit metabolic profiles that markedly differ from those of control individuals, supporting the notion that metabolites may serve as easily identifiable biomarkers for specific conditions. An emerging branch of metabolomics resulting from biomarker studies, however, involves the study of retinal metabolic dysfunction as causes of degeneration. Recent publications have identified a number of metabolic processes-including but not limited to glucose and oxygen metabolism-that, when perturbed, play a role in the degeneration of photoreceptor cells. As a result, such studies have led to further research elucidating methods for prolonging photoreceptor survival in an effort to halt degeneration in its early stages. This review will explore the ways in which metabolomics has deepened our understanding of the causes of retinal degeneration and discuss how metabolomics can be used to prevent retinal degeneration from progressing to its later disease stages. PMID: 29332245 [PubMed - as supplied by publisher]

Urinary metabolomics study the mechanism of Taohong Siwu Decoction intervention in acute blood stasis model rats based on liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2018 Jan 02;1074-1075:51-60 Authors: Zhang X, Li P, Hua Y, Ji P, Yao W, Ma Q, Yuan Z, Wen Y, Yang C, Wei Y Abstract Taohong Siwu Decoction (TSD) is a classic prescription in traditional Chinese medicine and is widely used to promote blood circulation to remove blood stasis. However, the effect mechanisms are not yet well understood. Here, a urinary metabolomic approach based on liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC/Q-TOF-MS) was conducted to explore the changes in the endogenous metabolites and to assess the integral efficacy of TSD on acute blood stasis model rats. Then, parameters for hemorheology and coagulation functions were detected. Principal component analysis (PCA) and orthogonal partial least squares discriminate analysis (OPLS-DA) was used to investigate the global metabolite alterations and to evaluate the preventive effects of TSD in rats. Potential metabolite markers were found using OPLS-DA and t-test. Furthermore, metabolic pathway analysis was performed to construct metabolic networks. The results showed that TSD could significantly decrease whole blood viscosity and plasma viscosity. It also significantly prolonged partial thromboplastin time (APPT) and prothrombin time (PT), increased thrombin time (TT) and lowered fibrinogen content (FIB). Moreover, 24 potential metabolite markers of acute blood stasis were screened, and the levels were all reversed to different degrees after TSD administration. In metabolic networks, amino acid metabolism (arginine and proline metabolism; histidine metabolism; alanine, aspartate, and glutamate metabolism; phenylalanine, tyrosine, and tryptophan biosynthesis; phenylalanine metabolism) and lipid metabolism (glycerophospholipid metabolism; linoleic acid metabolism; alpha-linolenic acid metabolism) were closely related with the intervention mechanism of TSD on acute blood stasis. The urinary metabolomic approach can be applied to clarify the mechanism of TSD in promoting blood circulation to remove acute blood stasis and to provide the theoretical basis for further research on the therapeutic mechanism of TSD in clinical practice. PMID: 29331744 [PubMed - as supplied by publisher]

Related Articles Hypoxia-Induced Metabolomic Alterations in Pancreatic Cancer Cells. Methods Mol Biol. 2018;1742:95-105 Authors: Gunda V, Kumar S, Dasgupta A, Singh PK Abstract Hypoxic conditions in the pancreatic tumor microenvironment lead to the stabilization of hypoxia-inducible factor-1 alpha (HIF-1α), which acts as the master regulator of cancer cell metabolism. HIF-1α-mediated metabolic reprogramming results in large-scale metabolite perturbations. Characterization of the metabolic intermediates and the corresponding metabolic pathways altered by HIF-1α would facilitate the identification of therapeutic targets for hypoxic microenvironments prevalent in pancreatic ductal adenocarcinoma and other solid tumors. Targeted metabolomic approaches are versatile in quantifying multiple metabolite levels in a single platform and, thus, enable the characterization of multiple metabolite alterations regulated by HIF-1α. In this chapter, we describe a detailed metabolomic approach for characterizing the hypoxia-induced metabolomic alterations using pancreatic cancer cell lines cultured in normoxic and hypoxic conditions. We elaborate the methodology of cell culture, hypoxic exposure, metabolite extraction, and relative quantification of polar metabolites from normoxia- and hypoxia-exposed cell extracts, using a liquid chromatography-coupled tandem mass spectrometry approach. Herein, using our metabolomic data, we also present the methods for metabolomic data representation. PMID: 29330793 [PubMed - in process]

Related Articles A Metabolomics Pilot Study on Desmoid Tumors and Novel Drug Candidates. Sci Rep. 2018 Jan 12;8(1):584 Authors: Mercier KA, Al-Jazrawe M, Poon R, Acuff Z, Alman B Abstract Desmoid tumors (aggressive fibromatosis) are locally invasive soft tissue tumors that lack the ability to metastasize. There are no directed therapies or standard treatment plan, and chemotherapeutics, radiation, and surgery often have temporary effects. The majority of desmoid tumors are related to T41A and S45F mutations of the beta-catenin encoding gene (CTNNB1). Using broad spectrum metabolomics, differences were investigated between paired normal fibroblast and desmoid tumor cells from affected patients. There were differences identified, also, in the metabolomics profiles associated with the two beta-catenin mutations, T41A and S45F. Ongoing drug screening has identified currently available compounds which inhibited desmoid tumor cellular growth by more than 50% but did not affect normal fibroblast proliferation. Two drugs were investigated in this study, and Dasatinib and FAK Inhibitor 14 treatments resulted in unique metabolomics profiles for the normal fibroblast and desmoid tumor cells, in addition to the T41A and S45F. The biochemical pathways that differentiated the cell lines were aminoacyl-tRNA biosynthesis in mitochondria and cytoplasm and signal transduction amino acid-dependent mTORC1 activation. This study provides preliminary understanding of the metabolic differences of paired normal and desmoid tumors cells, their response to desmoid tumor therapeutics, and new pathways to target for therapy. PMID: 29330550 [PubMed - in process]

Related Articles Missing Value Imputation Approach for Mass Spectrometry-based Metabolomics Data. Sci Rep. 2018 Jan 12;8(1):663 Authors: Wei R, Wang J, Su M, Jia E, Chen S, Chen T, Ni Y Abstract Missing values exist widely in mass-spectrometry (MS) based metabolomics data. Various methods have been applied for handling missing values, but the selection can significantly affect following data analyses. Typically, there are three types of missing values, missing not at random (MNAR), missing at random (MAR), and missing completely at random (MCAR). Our study comprehensively compared eight imputation methods (zero, half minimum (HM), mean, median, random forest (RF), singular value decomposition (SVD), k-nearest neighbors (kNN), and quantile regression imputation of left-censored data (QRILC)) for different types of missing values using four metabolomics datasets. Normalized root mean squared error (NRMSE) and NRMSE-based sum of ranks (SOR) were applied to evaluate imputation accuracy. Principal component analysis (PCA)/partial least squares (PLS)-Procrustes analysis were used to evaluate the overall sample distribution. Student's t-test followed by correlation analysis was conducted to evaluate the effects on univariate statistics. Our findings demonstrated that RF performed the best for MCAR/MAR and QRILC was the favored one for left-censored MNAR. Finally, we proposed a comprehensive strategy and developed a public-accessible web-tool for the application of missing value imputation in metabolomics ( https://metabolomics.cc.hawaii.edu/software/MetImp/ ). PMID: 29330539 [PubMed - in process]

Related Articles Uncovering the anticancer mechanism of Compound Kushen Injection against HCC by integrating quantitative analysis, network analysis and experimental validation. Sci Rep. 2018 Jan 12;8(1):624 Authors: Gao L, Wang KX, Zhou YZ, Fang JS, Qin XM, Du GH Abstract Compound Kushen Injection (CKI) is a Traditional Chinese Medicine (TCM) preparation that has been clinically used in China to treat various types of solid tumours. Although several studies have revealed that CKI can inhibit the proliferation of hepatocellular carcinoma (HCC) cell lines, the active compounds, potential targets and pathways involved in these effects have not been systematically investigated. Here, we proposed a novel idea of "main active compound-based network pharmacology" to explore the anti-cancer mechanism of CKI. Our results showed that CKI significantly suppressed the proliferation and migration of SMMC-7721 cells. Four main active compounds of CKI (matrine, oxymatrine, sophoridine and N-methylcytisine) were confirmed by the integration of ultra-performance liquid chromatography/mass spectrometry (UPLC-MS) with cell proliferation assays. The potential targets and pathways involved in the anti-HCC effects of CKI were predicted by a network pharmacology approach, and some of the crucial proteins and pathways were further validated by western blotting and metabolomics approaches. Our results indicated that CKI exerted anti-HCC effects via the key targets MMP2, MYC, CASP3, and REG1A and the key pathways of glycometabolism and amino acid metabolism. These results provide insights into the mechanism of CKI by combining quantitative analysis of components, network pharmacology and experimental validation. PMID: 29330507 [PubMed - in process]

Related Articles UHPLC-LTQ-Orbitrap-based metabolomics coupled with metabolomics pathway analysis method for exploring the protection mechanism of Kudiezi injection in a rat anti-ischemic cerebral reperfusion damage model. Chin J Nat Med. 2017 Dec;15(12):955-960 Authors: Liu SY, Cai W, Wang F, Liu Y, Shang ZP, Zhang XP, Wang ZJ, Lu JQ, Zhang JY Abstract Kudiezi injection has been used extensively in the treatment of cerebrovascular and cardiovascular diseases. However, its therapeutic effects and underlying mechanism of action are not fully understood. The aim of the present study was to clarify the protective mechanisms of Kudiezi injection on cerebral ischemic injury, using metabolomics methods. Middle cerebral artery occlusion (MCAO) was introduced in rats to build the cerebral ischemic damage. UHPLC-LTQ-Orbitrap-based analytical method was established for analysis of the metabolites. The raw mass data of all samples were normalized with Sieve 2.2 software and then introduced to orthogonal partial least squares discriminant analysis (OPLS-DA) model. Finally, 23 metabolites in plasma (15 were tentatively identified) were chosen as potential biomarkers, according to accurate mass measurements (< 5 ppm), MS/MS fragmentation patterns, and diagnostic product ions. Furthermore, on the basis of metabolic pathway analysis via metabolomics pathway analysis (MetPA), we first discovered that the protection mechanism in anti-ischemic cerebral reperfusion damage of Kudiezi injection was possibly related to the biosynthesis of phenylalanine, tyrosine, and tryptophan. The present study provided a useful approach for exploring the mechanism of ischemic stroke and evaluating the efficacy of Kudiezi injection or other traditional medicines. PMID: 29329654 [PubMed - in process]

38 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 2018/01/13PubMed 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.

Metabolome and proteome changes between biofilm and planktonic phenotypes of the marine bacterium Pseudoalteromonas lipolytica TC8. Biofouling. 2018 Jan 10;:1-17 Authors: Favre L, Ortalo-Magné A, Pichereaux C, Gargaros A, Burlet-Schiltz O, Cotelle V, Culioli G Abstract A number of bacteria adopt various lifestyles such as planktonic free-living or sessile biofilm stages. This enables their survival and development in a wide range of contrasting environments. With the aim of highlighting specific metabolic shifts between these phenotypes and to improve the overall understanding of marine bacterial adhesion, a dual metabolomics/proteomics approach was applied to planktonic and biofilm cultures of the marine bacterium Pseudoalteromonas lipolytica TC8. The liquid chromatography mass spectrometry (LC-MS) based metabolomics study indicated that membrane lipid composition was highly affected by the culture mode: phosphatidylethanolamine (PEs) derivatives were over-produced in sessile cultures while ornithine lipids (OLs) were more specifically synthesized in planktonic samples. In parallel, differences between proteomes revealed that peptidases, oxidases, transcription factors, membrane proteins and the enzymes involved in histidine biosynthesis were over-expressed in biofilms while proteins involved in heme production, nutrient assimilation, cell division and arginine/ornithine biosynthesis were specifically up-regulated in free-living cells. PMID: 29319346 [PubMed - as supplied by publisher]

Carnitine palmitoyltransferase 1C regulates cancer cell senescence through mitochondria-associated metabolic reprograming. Cell Death Differ. 2018 Jan 09;: Authors: Wang Y, Chen Y, Guan L, Zhang H, Huang Y, Johnson CH, Wu Z, Gonzalez FJ, Yu A, Huang P, Wang Y, Yang S, Chen P, Fan X, Huang M, Bi H Abstract Cellular senescence is a fundamental biological process that has profound implications in cancer development and therapeutics, but the underlying mechanisms remain elusive. Here we show that carnitine palmitoyltransferase 1C (CPT1C), an enzyme that catalyzes carnitinylation of fatty acids for transport into mitochondria for β-oxidation, plays a major role in the regulation of cancer cell senescence through mitochondria-associated metabolic reprograming. Metabolomics analysis suggested alterations in mitochondria activity, as revealed by the marked decrease in acylcarnitines in senescent human pancreatic carcinoma PANC-1 cells, indicating low CPT1C activity. Direct analyses of mRNA and protein show that CPT1C is significantly reduced in senescent cells. Furthermore, abnormal mitochondrial function was observed in senescent PANC-1 cells, leading to lower cell survival under metabolic stress and suppressed tumorigenesis in a mouse xenograft model. Knock-down of CPT1C in PANC-1 cells induced mitochondrial dysfunction, caused senescence-like growth suppression and cellular senescence, suppressed cell survival under metabolic stress, and inhibited tumorigenesis in vivo. Further, CPT1C knock-down suppressed xenograft tumor growth in situ. Silencing of CPT1C in five other tumor cell lines also caused cellular senescence. On the contrary, gain-of-function of CPT1C reversed PANC-1 cell senescence and enhanced mitochondrial function. This study identifies CPT1C as a novel biomarker and key regulator of cancer cell senescence through mitochondria-associated metabolic reprograming, and suggests that inhibition of CPT1C may represent a new therapeutic strategy for cancer treatment through induction of tumor senescence. PMID: 29317762 [PubMed - as supplied by publisher]

Beta-defensin 1, aryl hydrocarbon receptor and plasma kynurenine in major depressive disorder: metabolomics-informed genomics. Transl Psychiatry. 2018 Jan 10;8(1):10 Authors: Liu D, Ray B, Neavin DR, Zhang J, Athreya AP, Biernacka JM, Bobo WV, Hall-Flavin DK, Skime MK, Zhu H, Jenkins GD, Batzler A, Kalari KR, Boakye-Agyeman F, Matson WR, Bhasin SS, Mushiroda T, Nakamura Y, Kubo M, Iyer RK, Wang L, Frye MA, Kaddurah-Daouk R, Weinshilboum RM Abstract Major depressive disorder (MDD) is a heterogeneous disease. Efforts to identify biomarkers for sub-classifying MDD and antidepressant therapy by genome-wide association studies (GWAS) alone have generally yielded disappointing results. We applied a metabolomics-informed genomic research strategy to study the contribution of genetic variation to MDD pathophysiology by assaying 31 metabolites, including compounds from the tryptophan, tyrosine, and purine pathways, in plasma samples from 290 MDD patients. Associations of metabolite concentrations with depressive symptoms were determined, followed by GWAS for selected metabolites and functional validation studies of the genes identified. Kynurenine (KYN), the baseline plasma metabolite that was most highly associated with depressive symptoms, was negatively correlated with severity of those symptoms. GWAS for baseline plasma KYN concentrations identified SNPs across the beta-defensin 1 (DEFB1) and aryl hydrocarbon receptor (AHR) genes that were cis-expression quantitative trait loci (eQTLs) for DEFB1 and AHR mRNA expression, respectively. Furthermore, the DEFB1 locus was associated with severity of MDD symptoms in a larger cohort of 803 MDD patients. Functional studies demonstrated that DEFB1 could neutralize lipopolysaccharide-stimulated expression of KYN-biosynthesizing enzymes in monocytic cells, resulting in altered KYN concentrations in the culture media. In addition, we demonstrated that AHR was involved in regulating the expression of enzymes in the KYN pathway and altered KYN biosynthesis in cell lines of hepatocyte and astrocyte origin. In conclusion, these studies identified SNPs that were cis-eQTLs for DEFB1 and AHR and, which were associated with variation in plasma KYN concentrations that were related to severity of MDD symptoms. PMID: 29317604 [PubMed - in process]

Mitochondrial Network Responses in Oxidative Physiology and Disease. Free Radic Biol Med. 2018 Jan 06;: Authors: Go YM, Fernandes J, Hu X, Uppal K, Jones DP Abstract Mitochondrial activities are linked directly or indirectly to all cellular functions in aerobic eukaryotes. Omics methods enable new approaches to study functional organization of mitochondria and their adaptive and maladaptive network responses to bioenergetic fuels, physiologic demands, environmental challenges and aging. In this review, we consider mitochondria collectively within a multicellular organism as a macroscale "mitochondriome", functioning to organize bioenergetics and metabolism as an organism utilizes environmental resources and protects against environmental threats. We address complexities of knowledgebase-driven functional mapping of mitochondrial systems and then consider data-driven network mapping using omics methods. Transcriptome-metabolome-wide association study (TMWAS) shows connectivity and organization of nuclear transcription with mitochondrial transport systems in cellular responses to mitochondria-mediated toxicity. Integration of redox and respiratory measures with TMWAS shows central redox hubs separating systems linked to oxygen consumption rate and H2O2 production. Combined redox proteomics, metabolomics and transcriptomics further shows that physiologic network structures can be visualized separately from toxicologic networks. These data-driven integrated omics methods create new opportunities for mitochondrial systems biology. PMID: 29317273 [PubMed - as supplied by publisher]

Identification of potential sphingomyelin markers for the estimation of hematocrit in dried blood spots via a lipidomic strategy. Anal Chim Acta. 2018 Mar 20;1003:34-41 Authors: Liao HW, Lin SW, Lin YT, Lee CH, Kuo CH Abstract The dried blood spot (DBS) strategy is a convenient and minimally invasive approach to blood sampling. Due to its various advantages, this sampling technique has drawn significant attention in recent years. Hematocrit (HCT)-associated bias is one of the main obstacles that hinder wider DBS application in clinical practice. An accurate HCT estimation method could help calibrate HCT-associated bias and improve the quantification accuracy. This study used a lipidomics profiling strategy to identify HCT estimation markers using liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS), which provided advantages including the potential for the simultaneous measurements of target drug and HCT values. Three sphingomyelins (SMs), specifically SM 44:1, SM 44:2, and SM 44:3, were identified as potential HCT estimation markers. The proposed estimation markers were applied to 54 DBS samples collected from two sets of patients. The analytical results revealed that the estimation errors for all of the HCT values were less than 20%, which demonstrated the feasibility of using the proposed markers to estimate the HCT values for the DBS samples. We suggest that the proposed HCT markers could provide a new strategy for HCT estimation with higher convenience using an LC-ESI-MS platform, which could contribute to wider DBS applications in clinical practice. We also demonstrated that lipidomics is a promising strategy for the discovery of HCT estimation markers in DBS samples. PMID: 29317027 [PubMed - in process]