Discovery of serum biomarkers for diagnosis of tuberculosis by NMR metabolomics including cross-validation with a second cohort.

BACKGROUND: Tuberculosis (TB) is a disease with worldwide presence and a major cause of death in several developing countries. Current diagnostic methodologies often lack specificity and sensitivity, whereas a long time is needed to obtain a conclusive result. METHODS: In an effort to develop better diagnostic methods, this study aimed at the discovery of a biomarker signature for TB diagnosis using a Nuclear Magnetic Resonance based metabolomics approach. In this study, we acquired 1H NMR spectra of blood serum samples of groups of healthy subjects, individuals with latent TB and of patients with pulmonary and extra-pulmonary TB. The resulting data were treated with uni- and multivariate statistical analysis. RESULTS: Six metabolites (inosine, hypoxanthine, mannose, asparagine, aspartate and glutamate) were validated by an independent cohort, all of them related with metabolic processes described as associated with TB infection. CONCLUSION: The findings of the study are according with the WHO Target Product Profile recommendations for a triage test to rule-out active TB.

Active and prospective latent tuberculosis are associated with different metabolomic profiles: clinical potential for the identification of rapid and non-invasive biomarkers.

Although 23% of world population is infected with Mycobacterium tuberculosis (M. tb), only 5-10% manifest the disease. Individuals surely exposed to M. tb that remain asymptomatic are considered potential latent TB (LTB) cases. Such asymptomatic M. tb.-exposed individuals represent a reservoir for active TB cases. Although accurate discrimination and early treatment of patients with active TB and asymptomatic M. tb.-exposed individuals are necessary to control TB, identifying those individuals at risk of developing active TB still remains a tremendous clinical challenge. This study aimed to characterize the differences in the serum metabolic profile specifically associated to active TB infected individuals or to asymptomatic M. tb.-exposed population. Interestingly, significant changes in a specific set of metabolites were shared when comparing either asymptomatic house-hold contacts of active TB patients (HHC-TB) or active TB patients (A-TB) to clinically healthy controls (HC). Furthermore, this analysis revealed statistically significant lower serum levels of aminoacids such as alanine, lysine, glutamate and glutamine, and citrate and choline in patients with A-TB, when compared to HHC-TB. The predictive ability of these metabolic changes was also evaluated. Although further validation in independent cohorts and comparison with other pulmonary infectious diseases will be necessary to assess the clinical potential, this analysis enabled the discrimination between HHC-TB and A-TB patients with an AUC value of 0.904 (confidence interval 0.81-1.00, p-value < 0.0001). Overall, the strategy described in this work could provide a sensitive, specific, and minimally invasive method that could eventually be translated into a clinical tool for TB control.

GSK3-SCF(FBXW7) targets JunB for degradation in G2 to preserve chromatid cohesion before anaphase.

JunB, an activator protein-1 (AP-1) transcription factor component, acts either as a tumor suppressor or as an oncogene depending on the cell context. In particular, JunB is strongly upregulated in anaplastic lymphoma kinase (ALK)-positive anaplastic large cell lymphoma (ALCL) where it enhances cell proliferation. Although its overexpression is linked to lymphomagenesis, the mechanisms whereby JunB promotes neoplastic growth are still largely obscure. Here, we show that JunB undergoes coordinated phosphorylation-dependent ubiquitylation during the G2 phase of the cell cycle. We characterized a critical consensus phospho-degron that controls JunB turnover and identified GSK3 and SCF(FBXW7) as, respectively, the kinase and the E3 ubiquitin ligase responsible for its degradation in G2. Pharmacological or genetic inactivation of the GSK3-FBXW7-JunB axis induced accumulation of JunB in G2/M and entailed transcriptional repression of the DNA helicase DDX11, leading to premature sister chromatid separation. This abnormal phenotype due to dysregulation of the GSK3ß/JunB/DDX11 pathway is phenocopied in ALK-positive ALCL. Thus, our results reveal a novel mechanism by which mitosis progression and chromatid cohesion are regulated through GSK3/SCF(FBXW7)-mediated proteolysis of JunB, and suggest that JunB proteolysis in G2 is an essential step in maintaining genetic fidelity during mitosis.

Serum metabolome analysis by 1H-NMR reveals differences between chronic lymphocytic leukaemia molecular subgroups.

Chronic lymphocytic leukaemia (CLL) is a heterogeneous disease exhibiting variable clinical course and survival rates. Mutational status of the immunoglobulin heavy chain variable regions (IGHVs) of CLL cells offers useful prognostic information for high-risk patients, but time and economical costs originally prevented it from being routinely used in a clinical setting. Instead, alternative markers of IGHV status, such as zeta-associated protein (ZAP70) or messenger RNA levels are often used. We report a (1)H-NMR-based metabolomics approach to examine serum metabolic profiles of early stage, untreated CLL patients (Binet stage A) classified on the basis of IGHV mutational status or ZAP70. Metabolic profiles of CLL patients (n=29) exhibited higher concentrations of pyruvate and glutamate and decreased concentrations of isoleucine compared with controls (n=9). Differences in metabolic profiles between unmutated (UM-IGHV; n=10) and mutated IGHV (M-IGHV; n=19) patients were determined using partial least square discriminatory analysis (PLS-DA; R(2)=0.74, Q(2)=0.36). The UM-IGHV patients had elevated levels of cholesterol, lactate, uridine and fumarate, and decreased levels of pyridoxine, glycerol, 3-hydroxybutyrate and methionine concentrations. The PLS-DA models derived from ZAP70 classifications showed comparatively poor goodness-of-fit values, suggesting that IGHV mutational status correlates better with disease-related metabolic profiles. Our results highlight the usefulness of (1)H-NMR-based metabolomics as a potential non-invasive prognostic tool for identifying CLL disease-state biomarkers.

ABACUS, a direct method for protein NMR structure computation via assembly of fragments.

The ABACUS algorithm obtains the protein NMR structure from unassigned NOESY distance restraints. ABACUS works as an integrated approach that uses the complete set of available NMR experimental information in parallel and yields spin system typing, NOE spin pair identities, sequence specific resonance assignments, and protein structure, all at once. The protocol starts from unassigned molecular fragments (including single amino acid spin systems) derived from triple-resonance (1)H/(13)C/(15)N NMR experiments. Identifications of connected spin systems and NOEs precede the full sequence specific resonance assignments. The latter are obtained iteratively via Monte Carlo-Metropolis and/or probabilistic sequence selections, molecular dynamics structure computation and BACUS filtering (A. Grishaev and M. Llinás, J Biomol NMR 2004;28:1-10). ABACUS starts from scratch, without the requirement of an initial approximate structure, and improves iteratively the NOE identities in a self-consistent fashion. The procedure was run as a blind test on data recorded on mth1743, a 70-amino acid genomic protein from M. thermoautotrophicum. It converges to a structure in ca. 15 cycles of computation on a 3-GHz processor PC. The calculated structures are very similar to the ones obtained via conventional methods (1.22 A backbone RMSD). The success of ABACUS on mth1743 further validates BACUS as a NOESY identification protocol.

1H NMR structural characterization of a nonmitogenic, vasodilatory, ischemia-protector and neuromodulatory acidic fibroblast growth factor.

A shortened genetically engineered form of acidic fibroblast growth factor (aFGF), that includes amino acids 28-154 of the full-length sequence (154 residues) plus Met in substitution of Leu27, does not induce cell division even though it is recognized by the cell membrane receptor, triggers the early mitogenic events, and retains the neuromodulatory, vasoactive, and cardio- and neuroprotective properties of the native full-length molecule. Taken together, these properties make this truncated aFGF a promising compound in the treatment of a wide assortment of neurological and cardiovascular pathologies where aFGF mitogenic activity is dispensable. Differences in biological activities between the shortened aFGF and the wild-type form have been attributed to lack of stability, and to the specific amino acid sequence missing at the N-terminus. Here we show that this shortened aFGF form has a three-dimensional structure even more stable than the wild-type protein at the mitogenic assay conditions; that this structure is similar to that of the wild type except at site 1 of interaction with the cell membrane receptor; that its lack of mitogenic activity cannot be attributed to the specific missing sequence; and that the vasodilatory activity of aFGF seems impaired by alterations of the three-dimensional structure of site 2 of interaction with the cell membrane receptor.

Three-dimensional structure of acidic fibroblast growth factor in solution: effects of binding to a heparin functional analog.

Acidic and basic fibroblast growth factors (aFGF and bFGF; FGFs) are paradigms of a group of nine closely related proteins known as the fibroblast growth factor family. FGFs induce mitosis in most mesoderm- and neuroectoderm-derived cells, and appear to be involved in diseases caused by anomalous cell proliferation. In vitro assays show that binding to heparin-like glycosaminoglycans is required to elicit the mitogenic activity of these proteins. It has been shown that myo-inositol hexasulfate (MIHS) emulates heparin in the mitogenesis assays of aFGF, and a low-resolution three-dimensional structure in solution of this protein bound to MIHS has been reported. Here we describe the 1H-NMR three-dimensional structure in solution of the free aFGF. Comparison of this structure with that of the protein bound to MIHS, upgraded to a level of refinement equivalent to that of the free protein, shows that MIHS binding causes some slight conformational changes with an increase in the definition of the structure. In addition, amide exchange H/2H rates of the most protected protons, and exchange data of the intermediate and fast-exchanging ones show that the free protein is less stable (< or = 2 kcal/mol) and more flexible in terms of local unfolding equilibria, respectively, than the MIHS-bound one. Thus, MIHS binding to aFGF causes a decrease of its flexibility, which translates into an enhancement of the definition of its three-dimensional structure. The increase of aFGF rigidity affects regions that include those involved in recognizing the cell membrane receptor. Thus, our data suggest that enhancement of structural definition may play a key role in the modulation of the affinity of aFGF by its receptor, and, consequently, of its specific mitogenic activity.

X-ray structure of native full-length human fibroblast-growth factor at 0.25-nm resolution.

Acidic fibroblast-growth factor (aFGF) is one of the typical members of a group of nine polypeptides of relatively similar amino acid sequence known as the fibroblast-growth-factor family of proteins. Widely distributed throughout the organism, fibroblast-growth factors seem to be involved in numerous physiological processes ranging from control of cell proliferation and differentiation to modulation of animal behaviour and arterial blood pressure. This wide assortment of biological activities explains their involvement in numerous pathologies. Instability and low yields of the purified protein have precluded high-resolution structural studies of the physiological form of aFGF. Nevertheless, modifications introduced recently into the synthesis and purification procedures of this protein have allowed preparations of samples that, as shown here, are reliable substrates to obtain crystals suitable for X-ray-diffraction studies. These analyses have allowed us to elucidate the three-dimensional structure of the physiological form of human aFGF by molecular-replacement methods, from the previously reported structure of a shortened form of bovine aFGF that was stabilized by point-directed mutagenesis. The structure was refined at a resolution of 0.25 nm to an R factor of 20.4% for 13,109 reflections between 0.6 nm and 0.25 nm, with rmsd of 1.1 pm and 1.9 degrees from ideal bond lengths and bond angles, respectively. Human aFGF folds according to a beta-trefoil topology. This fold consist of six beta-strand pairs. Three of them form a six-stranded beta-barrel structure that is capped at one end by the other three pairs arranged in a triangular array. The N-terminus of aFGF up to residue Pro19 appears flexible in the structure and does not specifically interact with the rest of the molecule.

1H-NMR assignment and solution structure of human acidic fibroblast growth factor activated by inositol hexasulfate.

A major fragment of human acidic fibroblast growth factor of 132 amino acid residues is shown to be as active and stable as the 139 residue molecule initially described, and commonly used in physiological studies. It is shown that inositol hexasulfate is a good substitute for heparin in both activating and protecting acidic fibroblast growth factor. The complex between the shortened form of the protein and inositol hexasulfate was used to determine the structure of activated acidic fibroblast growth factor in solution. The 1H-NMR spectrum of the complex was totally assigned, and a low-resolution, three-dimensional structure of the protein computed. The global fold of the activated acidic fibroblast growth factor is similar to that proposed for a crystallized variant of the protein obtained by genetic engineering whose activity is not dependent on heparin. The inositol hexasulfate binds to the protein through the positively charged groups of Lys126, Lys127, Arg133 and Lys142 side-chains. The computed three-dimensional structure suggests that inositol hexasulfate may stabilize and activate the protein by conferring rigidity to the hairpin involving beta-strands 10 and 11.

Effect of low pH and heparin on the structure of acidic fibroblast growth factor.

Changes in the fluorescence of the single tryptophan of acidic fibroblast growth factor have been used to monitor the effect of low pH on the conformation of the molecule, and the consequences of heparin binding and high ionic strength under such conditions. These studies demonstrate that the conformation of the protein changes reversibly below pH 5, and that heparin, depending on the conditions, may either prevent that change or induce a new irreversible modification of the structure, which runs parallel to the partial inactivation of the protein. It is also demonstrated that secondary heparin-binding sites appear at low pH, which favor the formation of precipitates at some protein/heparin ratios. Precipitation and inactivation of fibroblast growth factor at low pH may hinder its wound-healing activity, since acidification seems frequent in wounds.