Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis

Over-representation analysis (ORA) is one of the commonest pathway analysis approaches used for the functional interpretation of metabolomics datasets. Despite the widespread use of ORA in metabolomics, the community lacks guidelines detailing its best-practice use. Many factors have a pronounced impact on the results, but to date their effects have received little systematic attention. Using five publicly available datasets, we demonstrated that changes in parameters such as the background set, differential metabolite selection methods, and pathway database used can result in profoundly different ORA results. The use of a non-assay-specific background set, for example, resulted in large numbers of false-positive pathways. Pathway database choice, evaluated using three of the most popular metabolic pathway databases (KEGG, Reactome, and BioCyc), led to vastly different results in both the number and function of significantly enriched pathways. Factors that are specific to metabolomics data, such as the reliability of compound identification and the chemical bias of different analytical platforms also impacted ORA results. Simulated metabolite misidentification rates as low as 4% resulted in both gain of false-positive pathways and loss of truly significant pathways across all datasets. Our results have several practical implications for ORA users, as well as those using alternative pathway analysis methods. We offer a set of recommendations for the use of ORA in metabolomics, alongside a set of minimal reporting guidelines, as a first step towards the standardisation of pathway analysis in metabolomics.     

Giardia lamblia: detection and characterization of calmodulin

Calmodulin was detected in Giardia lamblia by radioimmunoassay and cyclic AMP phosphodiesterase activation. This protein was purified to apparent homogeneity by fast protein liquid chromatography with a yield of 260 ng of calmodulin/mg of protozoan protein. Purity was established by gel electrophoresis, gel filtration, and ion exchange chromatography. The parasite calmodulin has properties characteristic of calmodulin isolated from other eukaryotes, e.g., an apparent molecular weight of 16.7 kD; activation in calcium dependent manner of bovine heart cyclic nucleotide phosphodiesterase; and sensitivity to known calmodulin antagonists.     

Cl- channel blockers NPPB and niflumic acid blunt Ca(2+)-induced erythrocyte 'apoptosis'.

Exposure to Ca2+ ionophore ionomycin, osmotic shock, oxidative stress and glucose depletion trigger cell shrinkage and scramblase-mediated phosphatidylserine exposure at the outer leaflet of the erythrocyte cell membrane. The effects are partially due to activation of GARDOS channels and subsequent cellular K+ loss leading not only to cell shrinkage but also participating in the triggering of erythrocyte scramblase. As conductive loss of K+ would depend on the parallel loss of anions we hypothesised that activation of scramblase is similarly dependent on the activity of Cl- channels. To test this hypothesis, we used Cl- channel blockers NPPB and niflumic acid. It is shown here that treatment of erythrocytes with 1 microM ionomycin leads to cellular K+ loss, decrease of hematocrit and decrease of forward scatter in FACS analysis reflecting cell shrinkage as well as increase of annexin positive cells reflecting phosphatidylserine exposure. Those events were significantly blunted in the presence of 100 microM NPPB by 34% (K+ loss), 45% (hematocrit), 32% (forward scatter) and 69% (annexin binding), or in the presence of 100 microM niflumic acid by 15% (forward scatter) and 45% (annexin binding), respectively. Moreover, oxidative stress triggered annexin binding which was again significantly inhibited (by 51%) in the presence of 100 microM NPPB. In conclusion, Cl- channels presumably participate in the regulation of erythrocyte 'apoptosis'.     

Methane production and sulfate reduction in two Appalachian peatlands

Anaerobic carbon mineralization was evaluated over a 1-year period in two Sphagnum-dominated peatlands, Big Run Bog, West Virginia, and Buckle's Bog, Maryland. In the top 35 cm of peat, mean rates of methane production, anaerobic carbon dioxide production, and sulfate reduction at Big Run Bog were 63,406 and 146 mol L^-1 d^-1, respectively, and at Buckle's Bog were 18, 486 and 104 mol L^-1 d^-1. Annual anaerobic carbon mineralization to methane and carbon dioxide at Big Run Bog and Buckle's Bog was 52.8 and 57.2 mol m^-2, respectively. Rates of methane production were similar to rates reported for other freshwater peatlands, but methane production accounted for only 11.7 and 2.8%, respectively, of the total anaerobic carbon mineralization at these two sites. Carbon dioxide production, resulting substantially from sulfate reduction, dominated anaerobic carbon mineralization. Considerable sulfate reduction despite low instantaneous dissolved sulfate concentrations (typically < 300 mol L^-1 of substrate) was apparently fueled by oxidation and rapid turnover of the reduced inorganic sulfur pool.The coincidence of high sulfate inputs to the Big Run Bog and Buckle's Bog watersheds through acid precipitation with the unexpected importance of sulfate reduction leads us to suggest a new hypothesis: peatlands not receiving high sulfate loading should exhibit low rates of anaerobic decomposition, and a predominance of methane production over sulfate reduction; however, if such peatlands become subjected to high rates of sulfur deposition, sulfate reduction may be enhanced as an anaerobic mineralization pathway with attendant effects on carbon balance and peat accumulation.     

Some properties of polyethylene glycol:phenylalanine ammonia-lyase adducts.

Methoxypolyethylene glycol of 5000 daltons (PEG) was attached covalently to phenylalanine ammonia-lyase from Rhodotorula glutinis. Attachment of sufficient quantities of PEG to phenylalanine ammonia-lyase substantially reduces immunological recognition and clearance of the conjugated enzyme in mice. The modified enzyme demonstrates altered catalytic properties such as shifts in the pH and temperature optima, an increase in the Michaelis-Menten constant, and a lowered Vmax in comparison with the native enzyme. PEG-phenylalanine ammonia-lyase has increased resistance to proteolytic digestion, particularly when in the presence of cinnamate, a competitive inhibitor, while the native enzyme is rapidly inactivated. In the ultracentrifuge PEG-phenylalanine ammonia-lyase exhibits a lower sedimentation rate than the unmodified enzyme, despite the fact that it is much larger. The electrophoretic mobility of PEG-phenylalanine ammonia-lyase is greatly decreased in comparison to the unmodified enzyme. PEG-phenylalanine ammonia-lyase had a much longer blood-circulating life in mice, both initially and after a number of injections, than did the native enzyme. PEG-phenylalanine ammonia-lyase was a good immunogen but a poor antigen in mice and rabbits, that is, it readily induced antibody formation, but reacted poorly in vitro with the antibodies that were formed against it.     

Stimulation of erythrocyte phosphatidylserine exposure by lead ions

Pb⁺ intoxication causes anemia that is partially due to a decreased life span of circulating erythrocytes. As shown recently, a Ca²⁺-sensitive erythrocyte scramblase is activated by osmotic shock, oxidative stress, and/or energy depletion, leading to exposure of phosphatidylserine at the erythrocyte surface. Because macrophages are equipped with phosphatidylserine receptors, they bind, engulf, and degrade phosphatidylserine-exposing cells. The present experiments were performed to explore whether Pb⁺ ions trigger phosphatidylserine exposure of erythrocytes. The phosphatidylserine exposure was estimated on the basis of annexin binding as determined using fluorescence-activated cell sorting (FACS) analysis. Exposure to Pb⁺ ions [0.1 µM Pb(NO₃)₂] significantly increased annexin binding. This effect was paralleled by erythrocyte shrinkage, which was apparent on the basis of the decrease in forward scatter in FACS analysis. The effect of Pb⁺ ions on cell volume was virtually abolished, and the effect of Pb⁺ ions on annexin binding was blunted after increase of extracellular K⁺ concentration. Moreover, both effects of Pb⁺ ions were partially prevented in the presence of clotrimazole (10 µM), an inhibitor of the Ca²⁺-sensitive K⁺ channels in the erythrocyte cell membrane. Whole cell patch-clamp experiments disclosed a significant activation of a K⁺-selective conductance after Pb⁺ ion exposure, an effect requiring higher (10 µM) concentrations, however. In conclusion, Pb⁺ ions activate erythrocyte K⁺ channels, leading to erythrocyte shrinkage, and also activate the erythrocyte scramblase, leading to phosphatidylserine exposure. The effect could well contribute to the reported decreased life span of circulating erythrocytes during Pb⁺ intoxication. cell volume; annexin; apoptosis; Gardos channel; calcium     

Stimulation of eryptosis by anti-A IgG antibodies.

Anti-A IgG antibodies have previously been shown to stimulate Ca(2+) entry into red blood cells. Increased cytosolic free Ca(2+) concentration is known to trigger eryptosis, i.e. suicidal erythrocyte death, characterized by exposure of phosphatidylserine at the erythrocyte surface. As macrophages are equipped with phosphatidylserine receptors, they bind, engulf and degrade phosphatidylserine exposing cells. The present experiments have been performed to explore whether anti-A IgGs trigger phosphatidylserine exposure of erythrocytes. Phosphatidylserine exposure was estimated from annexin-V binding as determined in FACS analysis. Exposure to anti-A IgGs (0.5 microg/ml) indeed significantly increased annexin-V binding in erythrocytes with blood group A, but not in erythrocytes with blood group 0. According to Fluo3 fluorescence, anti-A IgGs increased cytosolic Ca(2+) concentration. Whole cell patch clamp recordings revealed the activation of a Ca(2+)-permeable cation channel following treatment with anti-A-IgGs. Annexin-V binding following anti-A IgG exposure was blunted by Ca(2+) removal while anti-A IgG-stimulated cation channel activity was not dependent on extracellular Ca(2+). Osmotic shock (exposure of erythrocytes to 850 mOsm) increased annexin binding, an effect further enhanced by exposure to anti-A IgGs. In conclusion, anti-A IgGs activate erythrocyte cation channels leading to Ca(2+) entry and subsequent erythrocyte cell membrane scrambling. The effect most likely contributes to the elimination of erythrocytes following an immune reaction against the A antigen.     

Stimulation of suicidal erythrocyte death by methylglyoxal.

Diabetes increases the percentage of circulating erythrocytes exposing phosphatidylserine (PS) at the cell surface. PS-exposing erythrocytes are recognized, bound, engulfed and degraded by macrophages. Thus, PS exposure, a feature of suicidal erythrocyte death or eryptosis, accelerates clearance of affected erythrocytes from circulating blood. Moreover, PS-exposing erythrocytes bind to the vascular wall thus interfering with microcirculation. The present study explored mechanisms involved in the triggering of PS exposure by methylgloxal, an extra- and intracellular metabolite which is enhanced in diabetes. PS exposure, cell size and cytosolic Ca(2+)-activity after methylglyoxal treatment were measured by FACS analysis of annexin V binding, forward scatter and Fluo-3-fluorescence, respectively, and it was shown that the treatment significantly enhanced the percentage of PS-exposing erythrocytes at concentrations (0.3 microM) encountered in diabetic patients. Surprisingly, methylglyoxal did not significantly increase cytosolic Ca(2+) concentration, and at concentrations up to 3 microM, did not decrease the forward scatter. Instead, exposure to methylglyoxal inhibited glycolysis thus decreasing ATP and GSH concentrations. In conclusion, methylglyoxal impairs energy production and anti-oxidative defense, effects contributing to the enhanced PS exposure of circulating erythrocytes and eventually resulting in anemia and deranged microcirculation.