HCV genotypes are differently prone to the development of resistance to linear and macrocyclic protease inhibitors

Background

Because of the extreme genetic variability of hepatitis C virus (HCV), we analyzed whether specific HCV-genotypes are differently prone to develop resistance to linear and macrocyclic protease-inhibitors (PIs).

Methods

The study includes 1568 NS3-protease sequences, isolated from PI-naive patients infected with HCV-genotypes 1a (N = 621), 1b (N = 474), 2 (N = 72), 3 (N = 268), 4 (N = 54) 5 (N = 6), and 6 (N = 73). Genetic-barrier was calculated as the sum of nucleotide-transitions (score = 1) and/or nucleotide-transversions (score = 2.5) required for drug-resistance-mutations emergence. Forty-three mutations associated with PIs-resistance were analyzed (36A/M/L/G-41R-43S/V-54A/S/V-55A-Q80K/R/L/H/G-109K-138T-155K/Q/T/I/M/S/G/L-156T/V/G/S-158I-168A/H/T/V/E/I/G/N/Y-170A/T-175L). Structural analyses on NS3-protease and on putative RNA-models have been also performed.

Results

Overall, NS3-protease was moderately conserved, with 85/181 (47.0%) amino-acids showing <1% variability. The catalytic-triad (H57-D81-S139) and 6/13 resistance-associated positions (Q41-F43-R109-R155-A156-V158) were fully conserved (variability <1%). Structural-analysis highlighted that most of the NS3-residues involved in drug-stabilization were highly conserved, while 7 PI-resistance residues, together with selected residues located in proximity of the PI-binding pocket, were highly variable among HCV-genotypes. Four resistance-mutations (80K/G-36L-175L) were found as natural polymorphisms in selected genotypes (80K present in 41.6% HCV-1a, 100% of HCV-5 and 20.6% HCV-6; 80G present in 94.4% HCV-2; 36L present in 100% HCV-3-5 and >94% HCV-2-4; 175L present in 100% HCV-1a-3-5 and >97% HCV-2-4). Furthermore, HCV-3 specifically showed non-conservative polymorphisms (R123T-D168Q) at two drug-interacting positions. Regardless of HCV-genotype, 13 PIs resistance-mutations were associated with low genetic-barrier, requiring only 1 nucleotide-substitution (41R-43S/V-54A-55A-80R-156V/T: score = 1; 54S-138T-156S/G-168E/H: score = 2.5). By contrast, by using HCV-1b as reference genotype, nucleotide-heterogeneity led to a lower genetic-barrier for the development of some drug-resistance-mutations in HCV-1a (36M-155G/I/K/M/S/T-170T), HCV-2 (36M-80K-155G/I/K/S/T-170T), HCV-3 (155G/I/K/M/S/T-170T), HCV-4-6 (155I/S/L), and HCV-5 (80G-155G/I/K/M/S/T).

Conclusions

The high degree of HCV genetic variability makes HCV-genotypes, and even subtypes, differently prone to the development of PIs resistance-mutations. Overall, this can account for different responsiveness of HCV-genotypes to PIs, with important clinical implications in tailoring individualized and appropriate regimens.     

Bioinformatic analysis of pathogenic missense mutations of activin receptor like kinase 1 ectodomain

Activin A receptor, type II-like kinase 1 (also called ALK1), is a serine-threonine kinase predominantly expressed on endothelial cells surface. Mutations in its ACVRL1 encoding gene (12q11-14) cause type 2 Hereditary Haemorrhagic Telangiectasia (HHT2), an autosomal dominant multisystem vascular dysplasia. The study of the structural effects of mutations is crucial to understand their pathogenic mechanism. However, while an X-ray structure of ALK1 intracellular domain has recently become available (PDB ID: 3MY0), structure determination of ALK1 ectodomain (ALK1(EC)) has been elusive so far. We here describe the building of a homology model for ALK1(EC), followed by an extensive bioinformatic analysis, based on a set of 38 methods, of the effect of missense mutations at the sequence and structural level. ALK1(EC) potential interaction mode with its ligand BMP9 was then predicted combining modelling and docking data. The calculated model of the ALK1(EC) allowed mapping and a preliminary characterization of HHT2 associated mutations. Major structural changes and loss of stability of the protein were predicted for several mutations, while others were found to interfere mainly with binding to BMP9 or other interactors, like Endoglin (CD105), whose encoding ENG gene (9q34) mutations are known to cause type 1 HHT. This study gives a preliminary insight into the potential structure of ALK1(EC) and into the structural effects of HHT2 associated mutations, which can be useful to predict the potential effect of each single mutation, to devise new biological experiments and to interpret the biological significance of new mutations, private mutations, or non-synonymous polymorphisms.     

Abscisic Acid Activates the Murine Microglial Cell Line N9 through the Second Messenger Cyclic ADP-ribose

Abscisic acid (ABA) is a phytohormone regulating important functions in higher plants, notably responses to abiotic stress. Recently, chemical or physical stimulation of human granulocytes was shown to induce production and release of endogenous ABA, which activates specific cell functions. Here we provide evidence that ABA stimulates several functional activities of the murine microglial cell line N9 (NO and tumor necrosis factor-α production, cell migration) through the second messenger cyclic ADP-ribose and an increase of intracellular calcium. ABA production and release occur in N9 cells stimulated with bacterial lipopolysaccharide, phorbol myristate acetate, the chemoattractant peptide f-MLP, or β-amyloid, the primary plaque component in Alzheimer disease. Finally, ABA priming stimulates N9 cell migration toward β-amyloid. These results indicate that ABA is a pro-inflammatory hormone inducing autocrine microglial activation, potentially representing a new target for anti-inflammatory therapies aimed at limiting microglia-induced tissue damage in the central nervous system.Microglial cells are the monocyte/macrophage equivalent of the central nervous system and represent the first line of defense in the brain, by removing infectious agents and damaged cells (1). Microglia can also release a variety of trophic factors and cytokines able to regulate the communication between neuronal and other glial cells and can contribute to tissue repair and neuroprotection (2–4). Pathologic microglial activation, however, confers neurotoxic properties to these cells, thereby causing neuronal degeneration (5). Excessive activation of microglia, under conditions of chronic inflammation, can contribute to the pathogenesis of neurodegenerative diseases, such as multiple sclerosis and Alzheimer and Parkinson diseases, by producing and releasing a number of potentially cytotoxic substances, including pro-inflammatory cytokines and NO (4, 6–8). Therefore, identification of the molecular mechanisms underlying microglial activation might lead to the development of new anti-inflammatory drugs for the treatment of these diseases.Abscisic acid (ABA)² is a plant hormone regulating important biological functions in higher plants, including response to abiotic stress, control of stomatal closure, regulation of seed dormancy, and germination (9). Recently, ABA was shown to behave as an endogenous pro-inflammatory hormone in human granulocytes (10), stimulating several functional activities of these cells (migration, phagocytosis, reactive oxygen species, and NO production) through a signaling cascade that involves a protein kinase A-mediated ADP-ribosyl cyclase phosphorylation and consequent overproduction of the universal Ca²⁺ mobilizer cyclic ADP-ribose (cADPR) (11). This mechanism leads to an increase of the intracellular Ca²⁺ concentration, which is ultimately responsible for granulocyte activation (10).The facts that microglial cells play a defensive role in the central nervous system similar to that of granulocytes in other tissues and that cADPR has been described as the second messenger involved in the activation of microglia induced by lipopolysaccharide (LPS) (12) prompted us to investigate the effect of ABA in these cells.Indeed, exogenous ABA, at concentrations ranging from 250 nm to 20 μm, elicits functional activation of murine N9 cells, stimulating TNF-α release and cell migration through activation of the ADP-ribosyl cyclase CD38 and overproduction of cADPR. Moreover, N9 cells produce and release ABA when stimulated with LPS, amyloid β-peptide (βA), phorbol myristate acetate (PMA), or the chemoattractant peptide f-MLP. These results indicate that ABA behaves as an endogenous, pro-inflammatory hormone in murine microglia and provide a new target for future investigations into the role of this hormone in inflammatory and degenerative diseases of the central nervous system accompanied by microglial activation.     

Nitric oxide in the central nervous system: neuroprotection versus neurotoxicity

At the end of the 1980s, it was clearly demonstrated that cells produce nitric oxide and that this gaseous molecule is involved in the regulation of the cardiovascular, immune and nervous systems, rather than simply being a toxic pollutant. In the CNS, nitric oxide has an array of functions, such as the regulation of synaptic plasticity, the sleep-wake cycle and hormone secretion. Particularly interesting is the role of nitric oxide as a Janus molecule in the cell death or survival mechanisms in brain cells. In fact, physiological amounts of this gas are neuroprotective, whereas higher concentrations are clearly neurotoxic.     

The concerted action of the Helicobacter pylori cytotoxin VacA and of the v-ATPase proton pump induces swelling of isolated endosomes

The vacuolating cytotoxin (VacA) is a major virulence factor of Helicobacter pylori, the bacterium associated to gastroduodenal ulcers and stomach cancers. VacA induces formation of cellular vacuoles that originate from late endosomal compartments. VacA forms an anion-selective channel and its activity has been suggested to increase the osmotic pressure in the lumen of these acidic compartments, driving their swelling to vacuoles. Here, we have tested this proposal on isolated endosomes that allow one to manipulate at will the medium. We have found that VacA enhances the v-ATPase proton pump activity and the acidification of isolated endosomes in a Cl- dependent manner. Other counter-anions such as pyruvate, Br-, I- and SCN- can be transported by VacA with stimulation of the v-ATPase. The VacA action on isolated endosomes is associated with their increase in size. Single amino acid substituted VacA with no channel-forming and vacuolating activity is unable to induce swelling of endosomes. These data provide a direct evidence that the transmembrane VacA channel mediates an influx of anions into endosomes that stimulates the electrogenic v-ATPase proton pump, leading to their osmotic swelling and transformation into vacuoles.     

Influence of ring size on the cognition-enhancing activity of DM235 and MN19, two potent nootropic drugs

A series of analogs of DM235 and MN19, characterized by rings with different size, have been prepared and evaluated for their nootropic activity in the mouse passive-avoidance test. It was found that the optimal ring size for the analogs of DM235, showing endocyclic both amidic groups, is 6 or 7 atoms. For the compounds structurally related to MN19, carrying an exocyclic amide group, the piperidine ring is the moiety which gives the most interesting compounds.     

A metabonomic study of transgenic maize (Zea mays) seeds revealed variations in osmolytes and branched amino acids

The aim of the research was to investigate metabolic variations associated with genetic modifications in the grains of Zea mays using metabonomic techniques. With this in mind, the non-targeted characteristic of the technique is useful to identify metabolites peculiar to the genetic modification and initially undefined. The results obtained showed that the genetic modification, introducing Cry1Ab gene expression, induces metabolic variations involving the primary nitrogen pathway. Concerning the methodological aspects, the experimental protocol used has been applied in this field for the first time. It consists of a combination of partial least square-discriminant analysis and principal component analysis. The most important metabolites for discrimination were selected and the metabolic correlations linking them are identified. Principal component analysis on selected signals confirms metabolic variations, highlighting important details about the changes induced on the metabolic network by the presence of a Bt transgene in the maize genome.     

A new Late-glacial site with Picea abies in the northern Apennine foothills: an exception to the model of glacial refugia of trees

We describe a new palaeobotanical site at Bubano quarry on the easternmost Po plain, northern Italy. Pollen and macrofossils from river and marsh sediments demonstrate the occurrence of Picea in a Pinus sylvestris forest growing in a radius of some tens of kilometres south of the sedimentation place, at the beginning of the Late-glacial interstadial. The Late-glacial and Holocene history of Picea in the northern Apennines is reconstructed on the basis of the palaeobotanical record. The sharp climatic continentality increase eastwards across the northern Apennines from the Tyrrhenian to the Adriatic coast is considered significant for the survival of Picea during the Late-glacial. The most critical phase of survival is related to the moisture changes and consequent Abies competition associated with the last glacial-interglacial transition and the early Holocene. The residual spruce populations expanded during the middle Holocene. The history of Picea in the northern Apennines is a case of ineffective interglacial spread of tree populations from pre-existing stands of LGM (Last Glacial Maximum) and Late-glacial age.