Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry.

Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells coupled with systemic indicators of the host response to tumor development have the potential to yield blood profiles with clinical utility for diagnosis and monitoring of treatment. We report results from two separate studies using gas chromatography time-of-flight mass spectrometry (GC-TOF MS) to profile metabolites in human blood samples that significantly differ from non-small cell lung cancer (NSCLC) adenocarcinoma and other lung cancer cases. Metabolomic analysis of blood samples from the two studies yielded a total of 437 metabolites, of which 148 were identified as known compounds and 289 identified as unknown compounds. Differential analysis identified 15 known metabolites in one study and 18 in a second study that were statistically different (p-values <0.05). Levels of maltose, palmitic acid, glycerol, ethanolamine, glutamic acid, and lactic acid were increased in cancer samples while amino acids tryptophan, lysine and histidine decreased. Many of the metabolites were found to be significantly different in both studies, suggesting that metabolomics appears to be robust enough to find systemic changes from lung cancer, thus showing the potential of this type of analysis for lung cancer detection

Mobilization of pro-inflammatory lipids in obese Plscr3-deficient mice

Metabolic profiling of mice deficient in phospholipid scramblase 3 reveals a possible molecular link between obesity and inflammation

Pharmacometabolomics reveals racial differences in response to atenolol treatment.

Antihypertensive drugs are among the most commonly prescribed drugs for chronic disease worldwide. The response to antihypertensive drugs varies substantially between individuals and important factors such as race that contribute to this heterogeneity are poorly understood. In this study we use metabolomics, a global biochemical approach to investigate biochemical changes induced by the beta-adrenergic receptor blocker atenolol in Caucasians and African Americans. Plasma from individuals treated with atenolol was collected at baseline (untreated) and after a 9 week treatment period and analyzed using a GC-TOF metabolomics platform. The metabolomic signature of atenolol exposure included saturated (palmitic), monounsaturated (oleic, palmitoleic) and polyunsaturated (arachidonic, linoleic) free fatty acids, which decreased in Caucasians after treatment but were not different in African Americans (p<0.0005, q<0.03). Similarly, the ketone body 3-hydroxybutyrate was significantly decreased in Caucasians by 33% (p<0.0001, q<0.0001) but was unchanged in African Americans. The contribution of genetic variation in genes that encode lipases to the racial differences in atenolol-induced changes in fatty acids was examined. SNP rs9652472 in LIPC was found to be associated with the change in oleic acid in Caucasians (p<0.0005) but not African Americans, whereas the PLA2G4C SNP rs7250148 associated with oleic acid change in African Americans (p<0.0001) but not Caucasians. Together, these data indicate that atenolol-induced changes in the metabolome are dependent on race and genotype. This study represents a first step of a pharmacometabolomic approach to phenotype patients with hypertension and gain mechanistic insights into racial variability in changes that occur with atenolol treatment, which may influence response to the drug

Structure of the dsDNA bacteriophage HK97 and implications for capsid maturation

The structure of the HK97 head II empty particle was determined to 7 A resolution. The structure determination used molecular replacement averaging and phase extension. Averaging was initiated at very low (200-57 A) resolution, and phases were extended to 7 A. This is the first crystal structure of a dsDNA bacteriophage, and at 650 Ain diameter, one of the largest virus structures solved to date. The head II particle displays icosahedral (532) symmetry with strict T = 7 quasi symmetry. There are 420 copies of the capsid protein (gp5) arranged on the icosahedral lattice as pentamers and hexamers. The particle is shaped like an icosahedron with flat, triangular faces. The capsid shell is unusually thin, with an average dimension of 25 A. The gp5 monomer is composed largely of alpha helices, with two domains, one adjacent to the pentamer and hexamer axes (I) and the other forming a compact unit near the quasi threefold axes (II). There are a number of unusual features of the structure, particularly the alpha-helical fold of gp5. The arrangement of the subunits in the capsid shell conforms closely to a T = 7 surface lattice. This is the first crystal structure of a T = 7 virus with hexameric morphological units at hexavalent lattice points. dsDNA viruses assemble in a highly coordinated set of events. These events involve large conformational changes in secondary, tertiary and quaternary structures. The central feature of bacteriophage assembly occurs when dsDNA is packaged into the empty prohead shell, termed expansion . Expansion involves an increase in the capsid diameter and a dramatic conformational change in the capsid. The HK97 head II structure was used in combination with the cryo-EM reconstruction of the prohead II particle to understand the structural transitions during expansion. A model was built by docking the partial atomic model of head II into the prohead II cryo-EM reconstruction. The model shows that the central region of the hexamers are skewed by 22 A in the prohead, but the central region of the pentamer is unchanged. This central region is formed by domain I of head II gp5. Domains I and II are in different relative orientations in prohead and head particles. The prohead model and head II structure suggest a mechanism for particle maturation. The hexamers in the prohead are skewed into a dimer of trimers (domain I); during expansion the trimers slide relative to each other to form a 6-fold symmetric hexamer. The hexamers and pentamers in the prohead protrude from the capsid surface, and in the process of expansion, flatten out. Spectroscopy of the prohead and head particles indicates that there is a partial refolding, a 50% increase in the alpha-helical content of the capsid during the transition. The refolding may occur in domain II, which cannot be accommodated as a rigid body in prohead II. The model of particle maturation includes this large secondary structure change and the two domain motions: the un-skewing of the hexamer, the hinge motion of domain I relative to domain II

Macromolecular assembly: Chainmail stabilization of a viral capsid

AbstractThe subunits that make up the capsid of a double-stranded DNA phage have been found to be arranged as covalently bonded, interlinked pentamer and hexamer rings. This remarkable ‘chainmail’ arrangement raises interesting new questions about macromolecular assembly