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  • Open access
  • 145 Reads
Mitochondrial metabolomics reveals compartment-specific metabolic responses in yeast cells

Mutations in mitochondrial membrane proteins could cause physiological and metabolic alterations in mitochondria as well as in cytosol. In order to address the origin of these alterations, mitochondria and cytosol of yeast wild-type BY4741 and two mutants, sdh2Δ and atp4Δ, were isolated from whole cells. These three compartments, namely mitochondria, cytosol and whole cell, were analyzed by gas chromatography-mass spectrometry based metabolic profiling, identifying seventy-three metabolites altogether, from which sixteen or ten were not detected either in mitochondria or cytosol. Compartment-specific distribution and regulation of metabolites were observed, showing the responses to the deletions of sdh2 and atp4. Based on the metabolic signature in mitochondrial matrix and cytosol, both mutants can be discriminated from wild-type by principal component analysis. De letions of electron chain transport components, sdh2 and atp4, altered not only citrate cycle related metabolites, but also diverse metabolites including amino acids, fatty acids, purine and pyrimidine intermediates and others. By applying metabolomics to isolated mitochondria and cytosol, compartment-specific metabolic regulation can be identified, which is helpful in understanding the molecular mechanism of mitochondrial homeostasis in response to genetic mutations.

  • Open access
  • 138 Reads
Identification of Dietary Modulators of Cognitive Function in Ageing Using Metabolomics Discovery

With a global rise in ageing population and age-associated diseases, understanding how diet modifies cognitive ageing represents key revenues for prevention. Epidemiology suggests inverse associations between specific dietary patterns (i.e. Mediterranean diet) and cognitive decline and neurodegenerative diseases [1-3]- which raises an important question: which dietary bioactives (i.e. metabolites derived from plant foods) are capable of modulating neuronal ageing?

In this discovery (D-CogPlast6) study, we aim to identify a combination of diet-derived metabolites associated with cognitive decline using untargeted metabolomics. We leveraged the Three-City (3C) study (a large French cohort of elderly people) and compared the metabolic profiles of 209 individuals who later developed cognitive decline over 13 years against 209 controls with preserved cognition. Subjects were matched for age at baseline, gender and level of education. Serum samples (collected at the beginning of the cohort study when all participants were cognitively healthy) were profiled using high-resolution UHPLC-QToF (Bruker Impact ll) and raw UHPLC-MS data were processed using Galaxy ( Validated PLS-DA clearly distinguished between case and control populations. To account for the matched case-control study design and for potential confounders (i.e. season of blood sampling, body mass index, and number of medications consumed), sparse conditional logistic regression (with bootstrapped re-sampling) was adapted. 17 ions were representative of a serum metabolomic profile associated with cognition. These ions and their clusters whose intensities were significantly elevated in each of the population groups were annotated using online and in-house databases, literature search and commercial standards. Tandem MS/MS fragmentation is presently in progress for further validation of these ions’ identification.

Next, the robustness of this set of ions will be validated in a separate cohort of 400 subjects. The ability of these ions predictive of cognitive decline to modulate brain plasticity and neuronal integrity will be further investigated in an in vitro parabiosis assay and finally in a proof-of-principle dietary intervention mouse model. It is expected that these identified and validated biomarkers will lead to dietary intervention and recommendations for cognitive decline prevention.

6The D-CogPlast study is funded by JPI-HDHL and AgreenSkills+ Young incoming fellowship.



  1. Hardman, R.J., et al., Adherence to a Mediterranean-style diet and effects on cognition in adults: a qualitative evaluation and systemic review of longitudinal and prospective trials. Frontiers in Nutrition, 2016. 3(22): p. 1-13.
  2. Pelletier, A., et al., Mediterranean diet and preserved brain structural connectivity in older subjects. Alzheimer's & Dementia, 2015. 11(9): p. 1023-1031.
  3. Singh, B., et al., Association of mediterranean diet with mild cognitive impairment and Alzheimer's disease: a systematic review and meta-analysis. Journal of Alzheimer's Disease, 2014. 39(2): p. 271-282.
  • Open access
  • 157 Reads
ATP Metabolism in RBC as Potential Biomarker for Post-Exercise Hypotension and a Therapeutic Target for Cardiovascular Drugs

The importance of adenosine and ATP in regulating many biological functions has long been recognized, especially for their effects on the cardiovascular homeostasis which may be used for management of hypertension and cardiovascular diseases. In response to ischemia and cardiovascular injury, ATP is broken down to release adenosine. The activity of adenosine is very short lived because it is rapidly taken up by myocardial and endothelial cells, erythrocytes (RBC), and also rapidly metabolized to oxypurine metabolites and other adenine nucleotides. Extra-cellular and intracellular ATP is broken down rapidly to ADP and AMP and finally to adenosine by 5’-nucleotidase. These metabolic events are known to occur in the myocardium, endothelium as well as in RBC. Exercise has been shown to increase metabolism of ATP in the RBC which may be an important mechanism for post exercise hypotension and cardiovascular protection. The post exercise effect was greater in hypertensive than in normotensive rats. The review summarizes current evidence in support of ATP metabolism in the RBC as potential systemic biomarker for cardiovascular protection and toxicities. It also discusses the opportunities, challenges and obstacles of exploiting ATP metabolism in RBC as target for drug development.

  • Open access
  • 101 Reads
Metabolic shifts associated with postharvest storage of Kinnow (Citrus reticulata).

‘Kinnow’ Mandarin is highly prone to quality deterioration during postharvest storage which seriously affects consumer acceptability. In order to understand the biochemical basis for alterations in quality, a comprehensive evaluation of various metabolites was undertaken by storing fruits at low temperature (5°C) and ambient temperature (20°C) for 8 and 4 weeks, respectively. Sugars, organic acids, vitamins, polyphenolic, and limonoids were quantified through LC-MS/MS. While concentrations of glucose and fructose showed an increasing trend at ambient temperature; values reached a plateau by 14 days at low temperature. Organic acids, vitamin-B complex and C declined significantly during storage; however, the pattern of decline was more rapid at ambient temperature than low temperature. High limonin levels were observed in fruits stored at ambient temperature. Based on metabolites, it seems that ‘Kinnow’ fruits can be safely stored for 6 weeks at low temperature without any impairment in quality. Overall results strongly suggest that both duration and temperature of storage are essential in determining optimum shelf life. Thus, metabolite profiling is a useful tool for discriminating differences in metabolites of citrus fruits stored under different storage conditions.

  • Open access
  • 142 Reads
Metabolomic analysis revealed dose-dependent effects of algae feeding on redox balance, lipid, and microbial metabolism in mouse

Algae have been investigated and developed as a source of food, dietary supplement, and biofuel, due to their chemical and nutrient composition. However, the metabolic events in algae-elicited effects were not examined in details in spite of the fact that these benefits are largely based on the metabolic interactions between algal components and the biological system.  In this study, the influences of consuming green algae (Scenedesmus sp.) on the metabolic status of young mice was investigated through growth performance, blood chemistry, and liquid chromatography-mass spectrometry (LC-MS)-based metabolomics. Compared to the control diet, 5% algae promoted growth performance while 20% algae suppressed it. Serum glucose, triacylglycerols (TAG), and blood urea nitrogen (BUN) levels were not affected by both treatments, but serum cholesterol level was dramatically decreased by 20% algae feeding. Metabolomic analysis of liver, serum, feces and urine samples indicated that algae feeding greatly affected the metabolites belonging to amino acid, lipid, microbial metabolism and antioxidant system. The growth promotion effect of 5% algae feeding was associated with the increased levels of hepatic reduced glutathione, niacinamide, dephophocoenzyme A, and adenylsuccinic acid. In contrast, the growth suppression effects of 20% algae feeding was correlated to the increased level of oxidized glutathione and carnitine in the liver, increased EPA and DHA in liver and serum, and increased acyl-glycine in the urine. Overall, multiple correlations between metabolite markers and growth performance in algae feeding were established in this study and could serve as a foundation for further mechanistic investigations on the biological effects of algae feeding.

  • Open access
  • 232 Reads
Metabolic Alterations in Fumarate Hydratase Deficient Cells

Mutations of the tricarboxylic acid cycle (TCA cycle) enzyme fumarate hydratase (FH) cause the hereditary cancer syndrome Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC). FH-deficient renal cancers are highly aggressive and metastasise even when small, leading to an abysmal clinical outcome. How these cells survive without FH and how they become transformed is still under investigation. Today, I will show our data on the metabolic reprogramming triggered by the loss of FH, which induces, amongst various changes, the fumarate-mediated succination of the iron-sulfur-cluster proteins ISCU1, NFU1, and Bola1/3. Of note, this post translational modification leads to defects in iron-sulfur cluster biogenesis and complex I deficiency. These results could help to explain the profound alteration of mitochondrial metabolism in cells that lack FH.

  • Open access
  • 174 Reads
Nutrimetabolomics – a tool for humans and animals health management in "One Medicine" concept

Abstract: The field of metabolomics is still under development, but it has an increased capacity for research applications, especially in nutrition and health areas. The relationships between nutrients and the organisms functionality has increased interest for nutritional metabolomics researches. Nutrimetabolomics became thus more and more used for analyzing the correlation between dietary intake and diseases occurrence. On the other hand, metabolic fingerprinting can help for understanding and development of personalized nutrition. This could contribute to improvement of health status, well-being, animal growing or food security. The very close cohabitation of humans with animals, either for raising livestock for food, or as pets, makes most of the diseases known in medical sciences to be common to humans and animals. This makes nutrimetabolomics to be the key tool for confirming the medium-animal-human relationship in order to achieve an unitary health of the world. So, the aim of this review is to highlight the importance of nutrimetabolomics as main tool for both, human and veterinary medicine research.

  • Open access
  • 108 Reads
Clinical Metabolomics: An Integral Tool Driving Patient Phenotyping in Precision Medicine

Precision medicine is experiencing rapid growth and acceptance in the health-care landscape as a driving force for the future of medicine and is defined by the development of treatment strategies that are tailored to groups of patients based on specific biomarkers. Current precision medicine driven clinical trials assign patients to therapies based on the genetic alterations that are thought to be driving their diseases/cancers. BERG has validated the vision of Interrogative Biology® Platform to understand patients by “phenotype” rather than “genotype” by integrating molecular data directly from a patient with clinical and demographic information to develop artificial intelligence driven clinical trials. BERG is applying Bayesian causal inference to deconvolute unstructured clinical and molecular data and integrate this into models with cause and effect relationships that infers the health status of patients and outcome driven trials. This facilitates the generation of population cohorts for the discovery of biomarkers and drives personalized clinical decision-making. Development of in house Multi-omics platforms facilitates translation of targets and biomarkers in a rapid manner with the focus on cost, throughput, robustness, as well as translational utility into a R&D or CLIA lab setting. At BERG, we have implemented an industrial level high throughput metabolomics platform providing both high quality and depth of information allowing for reliable and broadest capture of the metabolome for the pre-clinical and clinical matrices analyzed. Metabolomics represents one of the most direct quantitative measurment to a patients phenotype to address the precision medicine maxim of treating the right patient, at the right time, with the right dose. Highlights of the BERG’s in-depth patient stratification approach as well as a route of complementary biomarker discovery will be presented.

  • Open access
  • 68 Reads
Untargeted metabolomics reveals specific withanolides and fatty acyl glycoside as tentative metabolites to differentiate organic and conventional Physalis peruviana fruits

The agronomic production systems may affect the levels of food metabolites. Metabolomics approaches have been applied as useful tools for the characterization of fruit metabolomes. In this study, metabolomics techniques were used to assess the differences in phytochemical composition between goldenberry samples produced by organic and conventional systems. To verify that the organic samples were free of pesticides, individual pesticides were analyzed.  Principal component analysis showed a clear separation of goldenberry samples from two different farming systems. Via targeted metabolomics assays, whereby carotenoids and ascorbic acid were analyzed, no statistical differences between both crops were found. Conversely, untargeted metabolomics allowed us to identify two withanolides and one fatty acyl glycoside as tentative metabolites that differentiate goldenberry fruits, with organic fruits having higher amounts of these compounds than conventional fruits. Hence, untargeted metabolomics technology could be a suitable tool to research differences of phytochemicals grown under different agricultural management practices, and to authenticate organic products.

  • Open access
  • 80 Reads
Metabolomics helps to unravel the mode of action of novel anti-malarial compounds

Access to large phenotypic screens has enabled the discovery of a number of compounds which can kill the malaria parasite in vitro. Translating these findings into new anti-malarial drugs faces a number of challenges. Finding the mode of action of these compounds can help in focussing efforts to develop the most promising compounds and help in designing new combination therapies targeting different pathways in the parasite to overcome drug-resistance. Using a microplate-based, untargeted metabolomics analysis of Plasmodium falciparum, we investigated the mode of action of 11 potent antimalarial compounds obtained from the Medicines for Malaria Venture and the Open Source Malaria project. This approach revealed significant metabolic perturbation associated with the most potent compounds, and identified the most likely pathways targeted by each compound. The major metabolic pathway intermediates which were found to be perturbed were from the pyrimidine biosynthesis pathway, glycolysis, phospholipid metabolism and haemoglobin degradation. Multivariate analyses allowed classification of some novel compounds that targeted the same biochemical pathways as two known anti-malarials, Atovaquone and Cipargamin. Interestingly, compounds showing similar biochemical activities did not always have similar chemical structures.  This study shows that a simple and efficient metabolomics assay can rapidly reveal the biochemical basis of the mode of action of newly discovered anti-malarials. This information can be used for prioritising compounds before progressing them through the optimization pipeline and further development. 

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