PubMed

Precision medicine screening using whole-genome sequencing and advanced imaging to identify disease risk in adults. Proc Natl Acad Sci U S A. 2018 Mar 19;: Authors: Perkins BA, Caskey CT, Brar P, Dec E, Karow DS, Kahn AM, Hou YC, Shah N, Boeldt D, Coughlin E, Hands G, Lavrenko V, Yu J, Procko A, Appis J, Dale AM, Guo L, Jönsson TJ, Wittmann BM, Bartha I, Ramakrishnan S, Bernal A, Brewer JB, Brewerton S, Biggs WH, Turpaz Y, Venter JC Abstract Reducing premature mortality associated with age-related chronic diseases, such as cancer and cardiovascular disease, is an urgent priority. We report early results using genomics in combination with advanced imaging and other clinical testing to proactively screen for age-related chronic disease risk among adults. We enrolled active, symptom-free adults in a study of screening for age-related chronic diseases associated with premature mortality. In addition to personal and family medical history and other clinical testing, we obtained whole-genome sequencing (WGS), noncontrast whole-body MRI, dual-energy X-ray absorptiometry (DXA), global metabolomics, a new blood test for prediabetes (Quantose IR), echocardiography (ECHO), ECG, and cardiac rhythm monitoring to identify age-related chronic disease risks. Precision medicine screening using WGS and advanced imaging along with other testing among active, symptom-free adults identified a broad set of complementary age-related chronic disease risks associated with premature mortality and strengthened WGS variant interpretation. This and other similarly designed screening approaches anchored by WGS and advanced imaging may have the potential to extend healthy life among active adults through improved prevention and early detection of age-related chronic diseases (and their risk factors) associated with premature mortality. PMID: 29555771 [PubMed - as supplied by publisher]

Non-targeted metabolomic biomarkers and metabotypes of type 2 diabetes: A cross-sectional study of PREDIMED trial participants. Diabetes Metab. 2018 Feb 20;: Authors: Urpi-Sarda M, Almanza-Aguilera E, Llorach R, Vázquez-Fresno R, Estruch R, Corella D, Sorli JV, Carmona F, Sanchez-Pla A, Salas-Salvadó J, Andres-Lacueva C Abstract AIM: To characterize the urinary metabolomic fingerprint and multi-metabolite signature associated with type 2 diabetes (T2D), and to classify the population into metabotypes related to T2D. METHODS: A metabolomics analysis using the 1H-NMR-based, non-targeted metabolomic approach was conducted to determine the urinary metabolomic fingerprint of T2D compared with non-T2D participants in the PREDIMED trial. The discriminant metabolite fingerprint was subjected to logistic regression analysis and ROC analyses to establish and to assess the multi-metabolite signature of T2D prevalence, respectively. Metabotypes associated with T2D were identified using the k-means algorithm. RESULTS: A total of 33 metabolites were significantly different (P<0.05) between T2D and non-T2D participants. The multi-metabolite signature of T2D comprised high levels of methylsuccinate, alanine, dimethylglycine and guanidoacetate, and reduced levels of glutamine, methylguanidine, 3-hydroxymandelate and hippurate, and had a 96.4% AUC, which was higher than the metabolites on their own and glucose. Amino-acid and carbohydrate metabolism were the main metabolic alterations in T2D, and various metabotypes were identified in the studied population. Among T2D participants, those with a metabotype of higher levels of phenylalanine, phenylacetylglutamine, p-cresol and acetoacetate had significantly higher levels of plasma glucose. CONCLUSION: The multi-metabolite signature of T2D highlights the altered metabolic fingerprint associated mainly with amino-acid, carbohydrate and microbiota metabolism. Metabotypes identified in this patient population could be related to higher risk of long-term cardiovascular events and therefore require further studies. Metabolomics is a useful tool for elucidating the metabolic complexity and interindividual variation in T2D towards the development of stratified precision nutrition and medicine. Trial registration at www.controlled-trials.com: ISRCTN35739639. PMID: 29555466 [PubMed - as supplied by publisher]

Related Articles Sequestration of polyunsaturated fatty acids in membrane phospholipids of Caenorhabditis elegans dauer larva attenuates eicosanoid biosynthesis for prolonged survival. Redox Biol. 2017 Aug;12:967-977 Authors: Lam SM, Wang Z, Li J, Huang X, Shui G Abstract Mechanistic basis governing the extreme longevity and developmental quiescence of dauer juvenile, a "non-ageing" developmental variant of Caenorhabditis elegans, has remained largely obscure. Using a lipidomic approach comprising multiple reaction monitoring transitions specific to distinct fatty acyl moieties, we demonstrated that in comparison to other developmental stages, the membrane phospholipids of dauer larva contain a unique enrichment of polyunsaturated fatty acids (PUFAs). Esterified PUFAs in phospholipids exhibited temporal accumulation throughout the course of dauer endurance, followed by sharp reductions prior to termination of diapause. Reductions in esterified PUFAs were accompanied by concomitant increases in unbound PUFAs, as well as their corresponding downstream oxidized derivatives (i.e. eicosanoids). Global phospholipidomics has unveiled that PUFA sequestration in membrane phospholipids denotes an essential aspect of dauer dormancy, principally via suppression of eicosanoid production; and a failure to upkeep membrane lipid homeostasis is associated with termination of dauer endurance. PMID: 28499251 [PubMed - indexed for MEDLINE]

Related Articles Shotgun lipidomics in substantiating lipid peroxidation in redox biology: Methods and applications. Redox Biol. 2017 Aug;12:946-955 Authors: Hu C, Wang M, Han X Abstract Multi-dimensional mass spectrometry-based shotgun lipidomics (MDMS-SL) has made profound advances for comprehensive analysis of cellular lipids. It represents one of the most powerful tools in analyzing lipids directly from lipid extracts of biological samples. It enables the analysis of nearly 50 lipid classes and thousands of individual lipid species with high accuracy/precision. The redox imbalance causes oxidative stress, resulting in lipid peroxidation, and alterations in lipid metabolism and homeostasis. Some lipid classes such as oxidized fatty acids, 4-hydroxyalkenal species, and plasmalogen are sensitive to oxidative stress or generated corresponding to redox imbalance. Therefore, accurate assessment of these lipid classes can provide not only the redox states, but also molecular insights into the pathogenesis of diseases. This review focuses on the advances of MDMS-SL in analysis of these lipid classes and molecular species, and summarizes their recent representative applications in biomedical/biological research. We believe that MDMS-SL can make great contributions to redox biology through substantiating the aberrant lipid metabolism, signaling, trafficking, and homeostasis under oxidative stress-related condition. PMID: 28494428 [PubMed - indexed for MEDLINE]

23 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 2018/03/20PubMed 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.

Knowledge-based metabolite annotation tool: CEU Mass Mediator. J Pharm Biomed Anal. 2018 Feb 23;154:138-149 Authors: Gil de la Fuente A, Godzien J, Fernández López M, Rupérez FJ, Barbas C, Otero A Abstract CEU Mass Mediator (CMM) is an on-line tool for aiding researchers when performing metabolite annotation. Its database is comprised of 279,318 real compounds integrated from several metabolomic databases including Human Metabolome Database (HMDB), KEGG and LipidMaps and 672,042 simulated compounds from MINE. In addition, CMM scores the annotations which matched the query parameters using 122 rules based on expert knowledge. This knowledge, obtained from the Centre for Metabolomics and Bioanalysis (CEMBIO) and from a literature review, enables CMM expert system to automatically extract evidence to support or refute the annotations by checking relationships among them. CMM is the first metabolite annotation tool that uses a knowledge-driven approach to provide support to the researcher. This allows to focus on the most plausible annotations, thus saving time and minimizing mistakes. PMID: 29547800 [PubMed - as supplied by publisher]

Metabolomic and oxidative effects of quantum dots-indolicidin on three generations of Daphnia magna. Aquat Toxicol. 2018 Mar 08;198:158-164 Authors: Falanga A, Mercurio FA, Siciliano A, Lombardi L, Galdiero S, Guida M, Libralato G, Leone M, Galdiero E Abstract This study evaluated the effect of QDs functionalized with the antimicrobial peptide indolicidin on oxidative stress and metabolomics profiles of Daphnia magna across three generations (F0, F1, and F2). Exposing D. magna to sub-lethal concentrations of the complex QDs-indolicidin, a normal survival of daphnids was observed from F0 to F2, but a delay of first brood, fewer broods per female, a decrease of length of about 50% compared to control. In addition, QDs-indolicidin induced a significantly higher production of reactive oxygen species (ROS) gradually in each generation and an impairment of enzymes response to oxidative stress such as superoxide dismutase (SOD), catalase (CAT) and glutathione transferase (GST). Effects were confirmed by metabolomics profiles that pointed out a gradual decrease of metabolomics content over the three generations and a toxic effect of QDs-indolicidin likely related to the higher accumulation of ROS and decreased antioxidant capacity in F1 and F2 generations. Results highlighted the capability of metabolomics to reveal an early metabolic response to stress induced by environmental QDs-indolicidin complex. PMID: 29547731 [PubMed - as supplied by publisher]

Metabolomics for improving pregnancy outcomes in women undergoing assisted reproductive technologies. Cochrane Database Syst Rev. 2018 Mar 16;3:CD011872 Authors: Siristatidis CS, Sertedaki E, Vaidakis D, Varounis C, Trivella M Abstract BACKGROUND: In order to overcome the low effectiveness of assisted reproductive technologies (ART) and the high incidence of multiple births, metabolomics is proposed as a non-invasive method to assess oocyte quality, embryo viability, and endometrial receptivity, and facilitate a targeted subfertility treatment. OBJECTIVES: To evaluate the effectiveness and safety of metabolomic assessment of oocyte quality, embryo viability, and endometrial receptivity for improving live birth or ongoing pregnancy rates in women undergoing ART, compared to conventional methods of assessment. SEARCH METHODS: We searched the Cochrane Gynaecology and Fertility Group Trials Register, CENTRAL, MEDLINE, Embase, CINAHL and two trial registers (Feburary 2018). We also examined the reference lists of primary studies and review articles, citation lists of relevant publications, and abstracts of major scientific meetings. SELECTION CRITERIA: Randomised controlled trials (RCTs) on metabolomic assessment of oocyte quality, embryo viability, and endometrial receptivity in women undergoing ART. DATA COLLECTION AND ANALYSIS: Pairs of review authors independently assessed trial eligibility and risk of bias, and extracted the data. The primary outcomes were rates of live birth or ongoing pregnancy (composite outcome) and miscarriage. Secondary outcomes were clinical pregnancy, multiple and ectopic pregnancy, cycle cancellation, and foetal abnormalities. We combined data to calculate odds ratios (ORs) for dichotomous data and 95% confidence intervals (CIs). Statistical heterogeneity was assessed using the I² statistic. We assessed the overall quality of the evidence for the main comparisons using GRADE methods. MAIN RESULTS: We included four trials with a total of 924 women, with a mean age of 33 years. All assessed the role of metabolomic investigation of embryo viability. We found no RCTs that addressed the metabolomic assessment of oocyte quality or endometrial receptivity.We found low-quality evidence of little or no difference between metabolomic and non-metabolomic assessment of embryos for rates of live birth or ongoing pregnancy (OR 1.02, 95% CI 0.77 to 1.35, I² = 0%; four RCTs; N = 924), live birth alone (OR 0.99, 95% CI 0.69 to 1.44, I² = 0%; three RCTs; N = 597), or miscarriage (OR 1.18, 95% CI 0.77 to 1.82; I² = 0%; three RCTs; N = 869). A sensitivity analysis excluding studies at high risk of bias did not change the interpretation of the results for live birth or ongoing pregnancy (OR 0.90, 95% CI 0.66 to 1.25, I² = 0%; two RCTs; N = 744). Our findings suggested that if the rate of live birth or ongoing pregnancy was 36% in the non-metabolomic group, it would be between 32% and 45% with the use of metabolomics.We found low-quality evidence of little or no difference between groups in rates of clinical pregnancy (OR 1.11, 95% CI 0.85 to 1.45; I²= 44%; four trials; N = 924) or multiple pregnancy (OR 1.50, 95% CI 0.70 to 3.19; I² = 0%; two RCTs, N = 180). Rates of cycle cancellation were higher in the metabolomics group (OR 1.78, 95% CI 1.18 to 2.69; I² = 51%; two RCTs; N = 744, low quality evidence). There was very low-quality evidence of little or no difference between groups in rates of ectopic pregnancy rates (OR 3.00, 95% CI 0.12 to 74.07; one RCT; N = 417), and foetal abnormality (no events; one RCT; N = 125). Data were lacking on other adverse effects. A sensitivity analysis excluding studies at high risk of bias did not change the interpretation of the results for clinical pregnancy (OR 1.03, 95% CI 0.76 to 1.38; I² = 40%; two RCTs; N = 744).The overall quality of the evidence ranged from very low to low. Limitations included serious risk of bias (associated with poor reporting of methods, attrition bias, selective reporting, and other biases), imprecision, and inconsistency across trials. AUTHORS' CONCLUSIONS: According to current trials in women undergoing ART, there is no evidence to show that metabolomic assessment of embryos before implantation has any meaningful effect on rates of live birth, ongoing pregnancy, miscarriage, multiple pregnancy, ectopic pregnancy or foetal abnormalities. The existing evidence varied from very low to low-quality. Data on other adverse events were sparse, so we could not reach conclusions on these. At the moment, there is no evidence to support or refute the use of this technique for subfertile women undergoing ART. Robust evidence is needed from further RCTs, which study the effects on live birth and miscarriage rates for the metabolomic assessment of embryo viability. Well designed and executed trials are also needed to study the effects on oocyte quality and endometrial receptivity, since none are currently available. PMID: 29547689 [PubMed - as supplied by publisher]

Metabolomics Identifies Distinctive Metabolite Signatures for Measures of Glucose Homeostasis: The Insulin Resistance Atherosclerosis Family Study (IRAS-FS). J Clin Endocrinol Metab. 2018 Mar 13;: Authors: Palmer ND, Okut H, Hsu FC, Ng MCY, Ida Chen YD, Goodarzi MO, Taylor KD, Norris JM, Lorenzo C, Rotter JI, Bergman RN, Langefeld CD, Wagenknecht LE, Bowden DW Abstract Context: Metabolomics provides a biochemical fingerprint which, when coupled with clinical phenotypes, can provide insight into physiological processes and disease. Objective: Survey metabolites associated with dynamic and basal measures of glucose homeostasis. Design: Analysis of 733 serum metabolites from the Insulin Resistance Atherosclerosis Family Study. Setting: Community-based. Participants: 1111 Mexican Americans. Main Outcome: Dynamic measures were obtained from the intravenous glucose tolerance test (FSIGT) and included insulin sensitivity (SI) and acute insulin response (AIRg). Basal measures included homeostatic model assessment of insulin resistance (HOMAIR) and beta-cell function (HOMAB). Results: SI was associated with 99 metabolites (P<6.82x10-5) explaining 28% of the variance (R2adj) beyond 28% by BMI. Beyond branched chain amino acids (BCAA; P=1.85x10-18-1.70x10-05, R2adj=8.1%) and phospholipids (P=3.51x10-17-3.00x10-05, R2adj=14%), novel signatures of long chain fatty acids (LCFAs; P=4.49x10-23-4.14x10-07, R2adj=11%) were observed. Conditional analysis suggested BCAA and LCFA signatures were independent. LCFAs were not associated with HOMAIR (P>0.024). AIRg was associated six metabolites; glucose had the strongest association (P=5.68x10-16). HOMAB had significant signatures from the urea cycle (P=9.64x10-14-7.27x10-06, R2adj=11%). Novel associations of poly unsaturated fatty acids (PUFA; P=2.58x10-13-6.70x10-05, R2adj=10%) and LCFA (P=9.06x10-15-3.93x10-07, R2adj=10%) were observed with glucose effectiveness (SG). Assessment of the hyperbolic relationship between insulin sensitivity and secretion through the disposition index (DI) revealed a distinctive signature of PUFA (P=1.55x10-12-5.81x10-06; R2adj=3.8%) beyond that of its component measures. Conclusions: Metabolomics reveals distinct signatures which differentiate dynamic and basal measures of glucose homeostasis and further identifies new metabolite classes associated with dynamic measures providing expanded insight into the metabolic basis of insulin resistance. . PMID: 29546329 [PubMed - as supplied by publisher]

Comprehensive Metabolic Profiling Reveals a Lipid-rich Fingerprint of Free Thyroxine Far Beyond Classical Parameters. J Clin Endocrinol Metab. 2018 Mar 12;: Authors: Lange T, Budde K, Homuth G, Kastenmüller G, Artati A, Krumsiek J, Völzke H, Adamski J, Petersmann A, Völker U, Nauck M, Friedrich N, Pietzner M Abstract Objective: Thyroid hormones are ubiqiutiously involved in human metabolism. However, the precise molecular patterns associated with alterations in thyroid hormones levels remain to be explored in detail. A number of recent studies took great advantage of metabolomics profiling to outline metabolic actions of thyroid hormones in humans. Methods: Among 952 participants of the Study of Health in Pomerania data on serum free thyroxine (FT4) and thyrotropin (TSH) as well as comprehensive (non-)targeted metabolomics data of plasma and urine samples were available. Linear regression analyses were performed to assess the association between FT4 or TSH and metabolite levels. Results and Conclusion: After accounting for major confounders 106 out of 613 plasma metabolites were significantly associated with FT4. Associations in urine were minor (12 out of 587). The majority of the plasma metabolites consisted of lipid species and subsequent analysis of highly resolved lipoprotein subclasses measured by 1H-NMR spectroscopy revealed a consistent decrease in varoius of these species (e.g. phospholipids) and large LDL- as well as small HDL-particles. The latter was unique to men. Several polyunsaturated and saturated fatty acids displayed an association with FT4 in women only. A random forest-based variable selection approach using phenotypic characteristics revealed higher alcohol intake in men and an adverse thyroid state as well as the menopause in women as putative mediating factors. In general, our observations confirmed the lipolytic and lipogenic effect of thyroid hormones even in the physiological range and revealed different phenotypic characteristics, e.g. lifestyle differences, as possible confounders for sex-specific findings. PMID: 29546278 [PubMed - as supplied by publisher]

Metabolic profiles of triple-negative and luminal A breast cancer subtypes in African-American identify key metabolic differences. Oncotarget. 2018 Feb 20;9(14):11677-11690 Authors: Tayyari F, Gowda GAN, Olopade OF, Berg R, Yang HH, Lee MP, Ngwa WF, Mittal SK, Raftery D, Mohammed SI Abstract Breast cancer, a heterogeneous disease with variable pathophysiology and biology, is classified into four major subtypes. While hormonal- and antibody-targeted therapies are effective in the patients with luminal and HER-2 subtypes, the patients with triple-negative breast cancer (TNBC) subtype do not benefit from these therapies. The incidence rates of TNBC subtype are higher in African-American women, and the evidence indicates that these women have worse prognosis compared to women of European descent. The reasons for this disparity remain unclear but are often attributed to TNBC biology. In this study, we performed metabolic analysis of breast tissues to identify how TNBC differs from luminal A breast cancer (LABC) subtypes within the African-American and Caucasian breast cancer patients, respectively. We used High-Resolution Magic Angle Spinning (HR-MAS) 1H Nuclear magnetic resonance (NMR) to perform the metabolomic analysis of breast cancer and adjacent normal tissues (total n=82 samples). TNBC and LABC subtypes in African American women exhibited different metabolic profiles. Metabolic profiles of these subtypes were also distinct from those revealed in Caucasian women. TNBC in African-American women expressed higher levels of glutathione, choline, and glutamine as well as profound metabolic alterations characterized by decreased mitochondrial respiration and increased glycolysis concomitant with decreased levels of ATP. TNBC in Caucasian women was associated with increased pyrimidine synthesis. These metabolic alterations could potentially be exploited as novel treatment targets for TNBC. PMID: 29545929 [PubMed]

Comprehensive subcellular topologies of polypeptides in Streptomyces. Microb Cell Fact. 2018 Mar 15;17(1):43 Authors: Tsolis KC, Tsare EP, Orfanoudaki G, Busche T, Kanaki K, Ramakrishnan R, Rousseau F, Schymkowitz J, Rückert C, Kalinowski J, Anné J, Karamanou S, Klapa MI, Economou A Abstract BACKGROUND: Members of the genus Streptomyces are Gram-positive bacteria that are used as important cell factories to produce secondary metabolites and secrete heterologous proteins. They possess some of the largest bacterial genomes and thus proteomes. Understanding their complex proteomes and metabolic regulation will improve any genetic engineering approach. RESULTS: Here, we performed a comprehensive annotation of the subcellular localization of the proteome of Streptomyces lividans TK24 and developed the Subcellular Topology of Polypeptides in Streptomyces database (SToPSdb) to make this information widely accessible. We first introduced a uniform, improved nomenclature that re-annotated the names of ~ 4000 proteins based on functional and structural information. Then protein localization was assigned de novo using prediction tools and edited by manual curation for 7494 proteins, including information for 183 proteins that resulted from a recent genome re-annotation and are not available in current databases. The S. lividans proteome was also linked with those of other model bacterial strains including Streptomyces coelicolor A3(2) and Escherichia coli K-12, based on protein homology, and can be accessed through an open web interface. Finally, experimental data derived from proteomics experiments have been incorporated and provide validation for protein existence or topology for 579 proteins. Proteomics also reveals proteins released from vesicles that bleb off the membrane. All export systems known in S. lividans are also presented and exported proteins assigned export routes, where known. CONCLUSIONS: SToPSdb provides an updated and comprehensive protein localization annotation resource for S. lividans and other streptomycetes. It forms the basis for future linking to databases containing experimental data of proteomics, genomics and metabolomics studies for this organism. PMID: 29544487 [PubMed - in process]

Related Articles Automatic untargeted metabolic profiling analysis coupled with Chemometrics for improving metabolite identification quality to enhance geographical origin discrimination capability. J Chromatogr A. 2018 Mar 16;1541:12-20 Authors: Han L, Zhang YM, Song JJ, Fan MJ, Yu YJ, Liu PP, Zheng QX, Chen QS, Bai CC, Sun T, She YB Abstract Untargeted metabolic profiling analysis is employed to screen metabolites for specific purposes, such as geographical origin discrimination. However, the data analysis remains a challenging task. In this work, a new automatic untargeted metabolic profiling analysis coupled with a chemometric strategy was developed to improve the metabolite identification results and to enhance the geographical origin discrimination capability. Automatic untargeted metabolic profiling analysis with chemometrics (AuMPAC) was used to screen the total ion chromatographic (TIC) peaks that showed significant differences among the various geographical regions. Then, a chemometric peak resolution strategy is employed for the screened TIC peaks. The retrieved components were further analyzed using ANOVA, and those that showed significant differences were used to build a geographical origin discrimination model by using two-way encoding partial least squares. To demonstrate its performance, a geographical origin discrimination of flaxseed samples from six geographical regions in China was conducted, and 18 TIC peaks were screened. A total of 19 significant different metabolites were obtained after the peak resolution. The accuracy of the geographical origin discrimination was up to 98%. A comparison of the AuMPAC, AMDIS, and XCMS indicated that AuMPACobtained the best geographical origin discrimination results. In conclusion, AuMPAC provided another method for data analysis. PMID: 29448994 [PubMed - indexed for MEDLINE]

Related Articles CLUH couples mitochondrial distribution to the energetic and metabolic status. J Cell Sci. 2017 Jun 01;130(11):1940-1951 Authors: Wakim J, Goudenege D, Perrot R, Gueguen N, Desquiret-Dumas V, Chao de la Barca JM, Dalla Rosa I, Manero F, Le Mao M, Chupin S, Chevrollier A, Procaccio V, Bonneau D, Logan DC, Reynier P, Lenaers G, Khiati S Abstract Mitochondrial dynamics and distribution are critical for supplying ATP in response to energy demand. CLUH is a protein involved in mitochondrial distribution whose dysfunction leads to mitochondrial clustering, the metabolic consequences of which remain unknown. To gain insight into the role of CLUH on mitochondrial energy production and cellular metabolism, we have generated CLUH-knockout cells using CRISPR/Cas9. Mitochondrial clustering was associated with a smaller cell size and with decreased abundance of respiratory complexes, resulting in oxidative phosphorylation (OXPHOS) defects. This energetic impairment was found to be due to the alteration of mitochondrial translation and to a metabolic shift towards glucose dependency. Metabolomic profiling by mass spectroscopy revealed an increase in the concentration of some amino acids, indicating a dysfunctional Krebs cycle, and increased palmitoylcarnitine concentration, indicating an alteration of fatty acid oxidation, and a dramatic decrease in the concentrations of phosphatidylcholine and sphingomyeline, consistent with the decreased cell size. Taken together, our study establishes a clear function for CLUH in coupling mitochondrial distribution to the control of cell energetic and metabolic status. PMID: 28424233 [PubMed - indexed for MEDLINE]

Rif1 phosphorylation site analysis in telomere length regulation and the response to damaged telomeres. DNA Repair (Amst). 2018 Mar 07;65:26-33 Authors: Wang J, Zhang H, Al Shibar M, Willard B, Ray A, Runge KW Abstract Telomeres, the ends of eukaryotic chromosomes, consist of repetitive DNA sequences and their bound proteins that protect the end from the DNA damage response. Short telomeres with fewer repeats are preferentially elongated by telomerase. Tel1, the yeast homolog of human ATM kinase, is preferentially recruited to short telomeres and Tel1 kinase activity is required for telomere elongation. Rif1, a telomere-binding protein, negatively regulates telomere length by forming a complex with two other telomere binding proteins, Rap1 and Rif2, to block telomerase recruitment. Rif1 has 14 SQ/TQ consensus phosphorylation sites for ATM kinases, including 6 in a SQ/TQ Cluster Domain (SCD) similar to other DNA damage response proteins. These 14 sites were analyzed as N-terminal, SCD and C-terminal domains. Mutating some sites to non-phosphorylatable residues increased telomere length in cells lacking Tel1 while a different set of phosphomimetic mutants increased telomere length in cells lacking Rif2, suggesting that Rif1 phosphorylation has both positive and negative effects on length regulation. While these mutations did not alter the sensitivity to DNA damaging agents, inducing telomere-specific damage by growing cells lacking YKU70 at high temperature revealed a role for the SCD. Mass spectrometry of Rif1 from wild type cells or those induced for telomere-specific DNA damage revealed increased phosphorylation in cells with telomere damage at an ATM consensus site in the SCD, S1351, and non-ATM sites S181 and S1637. A phosphomimetic rif1-S1351E mutation caused an increase in telomere length at synthetic telomeres but not natural telomeres. These results indicate that the Rif1 SCD can modulate Rif1 function. As all Rif1 orthologs have one or more SCD domains, these results for yeast Rif1 have implications for the regulation of Rif1 function in humans and other organisms. PMID: 29544213 [PubMed - as supplied by publisher]

Metabolomic association between venous thromboembolism in critically ill trauma patients and kynurenine pathway of tryptophan metabolism. Thromb Res. 2018 Mar 08;165:6-13 Authors: Voils SA, Shahin MH, Garrett TJ, Frye RF Abstract OBJECTIVE: Incidence of venous thromboembolism (VTE) in critically ill patients remains unacceptably high despite widespread use of thromboprophylaxis. A systems biology approach may be useful in understanding disease pathology and predicting response to treatment. Metabolite profile under specific environmental conditions provides the closest link to phenotype, but the relationship between metabolomics and risk of VTE in critically ill patients is unknown. In this study, metabolomics signatures are compared in patients with and without VTE. DESIGN: Multicenter case-control study using prospectively collected data from the Inflammation and Host Response to Injury program, with pathway and in silico gene expression analyses. SETTING: Eight level 1 US trauma centers. PATIENTS: Critically ill adults with blunt trauma who developed VTE within the first 28 days of hospitalization compared to patients without VTE (N-VTE). INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Patients included in the study (n = 20 VTE, n = 20 N-VTE) were mean age of 34 years, injury severity score of 35, and VTE diagnosed a median of 10.5 days after admission. Global metabolomics revealed two kynurenine metabolites, N-formylkynurenine (AUC = 0.77; 95% CI: 0.59-0.89) and 5-hydroxy-N-formylkynurenine (AUC = 0.80; 95% CI:0.63-0.90) significantly discriminated VTE and N-VTE; ratio between N-formylkynurenine/5-hydroxy-N-formylkynurenine improved predictive power (AUC = 0.87; 95% CI: 0.74-0.95). In the pathway analysis, tryptophan was the only significant metabolic pathway including N-formylkynurenine and 5-hydroxy-N-formylkynurenine (p < 0.001), and 8 proteins directly or indirectly interacted with these metabolites in the interaction network analysis. Of the 8 genes tested in the in silico gene expression analyses, KYNU (p < 0.001), CCBL1 (p < 0.001), and CCBL2 (p = 0.001) were significantly different between VTE and N-VTE, controlling for age and sex. CONCLUSIONS: Two novel kynurenine metabolites in the tryptophan pathway associated with hospital-acquired VTE, and 3 candidate genes were identified via pathway and interaction network analyses. Future studies are warranted to validate these findings in diverse populations using a multi-omics approach. PMID: 29544199 [PubMed - as supplied by publisher]

Prediction of platinum-based chemotherapy efficacy in lung cancer based on LC-MS metabolomics approach. J Pharm Biomed Anal. 2018 Feb 23;154:95-101 Authors: Peng F, Liu Y, He C, Kong Y, Ouyang Q, Xie X, Liu T, Liu Z, Peng J Abstract Lung cancer is the common cause of cancer-related death worldwide. Platinum-based chemotherapy is the cornerstone of treatment for lung cancer. Platinum sensitivity is a major possibility for effective cancer treatment. In this study, several potential biomarkers were identified for evaluating and predicting the response to platinum-based chemotherapy. LC-MS-based metabolomics was performed on plasma samples from 43 lung cancer patients with different chemotherapy efficacy. By combing multivariate statistical analysis, pathway analysis with correlation analysis, 8 potential biomarkers were significantly associated with platinum chemotherapy response. Moreover, a prediction model with these biomarkers involved in citric acid cycle, glutamate metabolism and amino acid metabolism, showed 100% sensitivity and 100% specificity for predicting chemotherapy response in a validation set. Interestingly, 2-hydroxyglutaric acid (2-HG) as an oncometabolite accumulated in lung cancer was remarkably elevated in the partial response (PR) patients. Collectively, our findings implicated that metabolomics can serve as a potential tool to select lung cancer patients that are more likely to benefit from the platinum-based treatment. PMID: 29544107 [PubMed - as supplied by publisher]

CRH/CRHR1 mediates prenatal synthetic glucocorticoid programming of depression-like behavior across 2 generations. FASEB J. 2018 Mar 15;:fj201700948RR Authors: Xu YJ, Sheng H, Wu TW, Bao QY, Zheng Y, Zhang YM, Gong YX, Lu JQ, You ZD, Xia Y, Ni X Abstract Pregnant women at risk of preterm labor usually receive synthetic glucocorticoids (sGCs) to promote fetal lung development. Emerging evidence indicates that antenatal sGC increases the risk of affective disorders in offspring. Data from animal studies show that such disorders can be transmitted to the second generation. However, the molecular mechanisms underlying the intergenerational effects of prenatal sGC remain largely unknown. Here we show that prenatal dexamethasone (Dex) administration in late pregnancy induced depression-like behavior in first-generation (F1) offspring, which could be transmitted to second-generation (F2) offspring with maternal dependence. Moreover, corticotropin-releasing hormone (CRH) and CRH receptor type 1 (CRHR1) expression in the hippocampus was increased in F1 Dex offspring and F2 offspring from F1 Dex female rats. Administration of a CRHR1 antagonist to newborn F1 Dex offspring alleviated depression-like behavior in these rats at adult. Furthermore, we demonstrated that increased CRHR1 expression in F1 and F2 offspring was associated with hypomethylation of CpG islands in Crhr1 promoter. Our results revealed that prenatal sGC exposure could program Crh and Crhr1 gene expression in hippocampus across 2 generations, thereby leading to depression-like behavior. Our study indicates that prenatal sGC can cause epigenetic instability, which increases the risk of disease development in the offspring's later life.-Xu, Y.-J., Sheng, H., Wu, T.-W., Bao, Q.-Y., Zheng, Y., Zhang, Y.-M., Gong, Y.-X., Lu, J.-Q., You, Z.-D., Xia, Y., Ni, X. CRH/CRHR1 mediates prenatal synthetic glucocorticoid programming of depression-like behavior across 2 generations. PMID: 29543532 [PubMed - as supplied by publisher]

1H NMR metabolic profiling of gastric cancer patients with lymph node metastasis. Metabolomics. 2018;14(4):47 Authors: Zhang H, Cui L, Liu W, Wang Z, Ye Y, Li X, Wang H Abstract Introduction: Gastric cancer (GC) is a malignant tumor worldwide. As primary pathway for metastasis, the lymphatic system is an important prognostic factor for GC patients. Although the metabolic changes of gastric cancer have been investigated in extensive studies, little effort focused on the metabolic profiling of lymph node metastasis (LNM)-positive or negative GC patients. Objectives: We performed 1H NMR spectrum of GC tissue samples with and without LNM to identify novel potential metabolic biomarkers in the process of LNM of GC. Methods: 1H NMR-based untargeted metabolomics approach combined with multivariate statistical analyses were used to study the metabolic profiling of tissue samples from LNM-positive GC patients (n = 40), LNM-negative GC patients (n = 40) and normal controls (n = 40). Results: There was a clear separation between GC patients and normal controls, and 33 differential metabolites were identified in the study. Moreover, GC patients were also well-classified according to LNM-positive or negative. Totally eight distinguishing metabolites were selected in the metabolic profiling of GC patients with LNM-positive or negative, suggesting the metabolic dysfunction in the process of LNM. According to further validation and analysis, especially BCAAs metabolism (leucine, isoleucine, valine), GSH and betaine may be as potential factors of diagnose and prognosis of GC patients with or without LNM. Conclusion: To our knowledge, this is the first metabolomics study focusing on LNM of GC. The identified distinguishing metabolites showed a promising application on clinical diagnose and therapy prediction, and understanding the mechanism underlying the carcinogenesis, invasion and metastasis of GC. PMID: 29541009 [PubMed]

Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A. Sci Rep. 2018 Mar 14;8(1):4505 Authors: Shahid M, Gull N, Yeon A, Cho E, Bae J, Yoon HS, You S, Yoon H, Kim M, Berman BP, Kim J Abstract Interstitial cystitis (IC) is a chronic urinary tract disease that is characterized by unpleasant sensations, such as persistent pelvic pain, in the absence of infection or other identifiable causes. We previously performed comprehensive metabolomics profiling of urine samples from IC patients using nuclear magnetic resonance and gas-chromatography/mass spectrometry and found that urinary α-oxoglutarate (α-OG), was significantly elevated. α-OG, a tricarboxylic acid (TCA) cycle intermediate, reportedly functions to suppress the proliferation of immortalized normal human bladder epithelial cells. Here, we identified AT-rich interactive domain 1 A (ARID1A), a key chromatin remodeler, as being hypomethylated and upregulated by α-OG treatment. This was done through EPIC DNA methylation profiling and subsequent biochemical approaches, including quantitative RT-PCR and western blot analyses. Furthermore, we found that α-OG almost completely suppresses ten-eleven translocation (TET) activity, but does not affect DNA methyltransferase (DNMT) activity. Altogether, our studies reveal the potential role of α-OG in epigenetic remodeling through its effects on ARID1A and TET expression in the bladder. This may provide a new possible therapeutic strategy in treating IC. PMID: 29540744 [PubMed - in process]