Cell protection, resistance and invasiveness of two malignant mesotheliomas as assessed by 10K-microarray

Malignant pleural mesothelioma (MPM) is an aggressive serosal tumor, strongly associated with former exposure to asbestos fibers and for which there is currently no effective treatment available. In human, MPM is characterized by a high local invasiveness, poor prognosis and therapeutic outcomes. In order to assess molecular changes that specify this phenotype, we performed a global gene expression profiling of human MPM. Using a 10,000-element microarray, we analyzed mRNA relative gene expression levels by comparing a mesothelioma cell line to either a pleural cell line or tumor specimens. To analyze these gene expression data, we used various bioinformatics softwares. Hierarchical clustering methods were used to group genes and samples with similar expression in an unsupervised mode. Genes of known function were further sorted by enzyme, function and pathway clusters using a supervised software (IncyteGenomics). Taken together, these data defined a molecular fingerprint of human MPM with more than 700 up- or down-regulated genes related to several traits of the malignant phenotype, specially associated with MPM invasiveness, protection and resistance to anticancer defenses. This portrait is meaningful in disease classification and management, and relevant in finding new specific markers of MPM. These molecular markers should improve the accuracy of mesothelioma diagnosis, prognosis and therapy.     

Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1

Abdominal aortic aneurysm (AAA) is a common cause of morbidity and mortality and has a significant heritability. We carried out a genome-wide association discovery study of 1866 patients with AAA and 5435 controls and replication of promising signals (lead SNP with a p value < 1 × 10⁻⁵) in 2871 additional cases and 32,687 controls and performed further follow-up in 1491 AAA and 11,060 controls. In the discovery study, nine loci demonstrated association with AAA (p < 1 × 10⁻⁵). In the replication sample, the lead SNP at one of these loci, rs1466535, located within intron 1 of low-density-lipoprotein receptor-related protein 1 (LRP1) demonstrated significant association (p = 0.0042). We confirmed the association of rs1466535 and AAA in our follow-up study (p = 0.035). In a combined analysis (6228 AAA and 49182 controls), rs1466535 had a consistent effect size and direction in all sample sets (combined p = 4.52 × 10⁻¹⁰, odds ratio 1.15 [1.10–1.21]). No associations were seen for either rs1466535 or the 12q13.3 locus in independent association studies of coronary artery disease, blood pressure, diabetes, or hyperlipidaemia, suggesting that this locus is specific to AAA. Gene-expression studies demonstrated a trend toward increased LRP1 expression for the rs1466535 CC genotype in arterial tissues; there was a significant (p = 0.029) 1.19-fold (1.04–1.36) increase in LRP1 expression in CC homozygotes compared to TT homozygotes in aortic adventitia. Functional studies demonstrated that rs1466535 might alter a SREBP-1 binding site and influence enhancer activity at the locus. In conclusion, this study has identified a biologically plausible genetic variant associated specifically with AAA, and we suggest that this variant has a possible functional role in LRP1 expression.     

Eye-specific segregation of optic afferents in mammals,fish, and frogs: The role of activity

Eye-specific patches or stripes normally develop in the visual cortex and superior colliculus of many (but not all) mammals and are also formed, after surgically produced binocular innervation, in the optic tectum of fish and frogs. The segregation of ocular dominance patches or columns has been studied using a variety of anatomical pathway-tracing techniques, by electrophysiological recording of postsynaptic units or field potentials, and by the 2-deoxyglucose method following visual stimulation of only one eye. In the tectum of both fish and frogs and in the cortex and colliculus of mammals, eye-specific patches develop from initially diffuse, overlapping projections. Of the various mechanisms that might cause such segregation, the evidence favors an activity-dependent process that stabilizes synapses from the same eye because of their correlated activity. First, several environmental manipulations affect the segregation of afferents in visual cortex: strabismus and alternate monocular exposure apparently enhance segregation, whereas dark rearing slows the segregation process, and monocular deprivation causes the experienced eye to form larger patches at the expense of those of the deprived eye. Second, blocking activity in both eyes is effective in preventing the segregation both in the tectum of fish and frog and in the visual cortex of cat. With the eyes blocked, alternate stimulation of the optic nerves permits the segregation of ocular dominance, at least onto single cells in the cat visual cortex. These findings are discussed in terms of an activity-dependent stabilization of those synapses having correlated activity (those from neighboring ganglion cells within one eye) but not of those lacking correlated activity (those from left and right eyes). We suggest that the eye-specific patches represent a compromise between total segregation of the projections from the two eyes and the formation of a single continuous retinotopic map across the surface of the cortex or tectum.     

Mechanism of action of Clostridium difficile toxin B: role of external medium and cytoskeletal organization in intoxicated cells

Toxin B, an exotoxin produced by Clostridium difficile, induces the rounding-up and arborization of cultured mammalian cells, a typical effect which resembles that provoked by cytochalasins. In this study, the effect of toxin B was examined on astroglial cells grown in primary culture. A specific antiserum to toxin B was used to investigate its mechanisms of action. We found that the toxin exerts its effects on cell morphology after its incorporation into cells. The internalization of toxin B requires the presence of calcium ions in the extracellular medium. Replacement of NaCl with sucrose or with potassium glutamate prevents the internalization of the toxin. The direct introduction of calcium ions into cells by the calcium ionophore A23187 stimulates toxin-induced morphological changes. In contrast, toxin-induced morphological transformations were prevented in cells treated with tumor-promoting phorbol. esters or with dibutyryl-cAMP, although such treatment did not abolish the internalization of the toxin. As in the other cell types, the earliest effect of toxin B on astrocyte cytoskeleton is the disruption of actin filaments, without no visible alteration of intermediate filament nor microtubule networks. As astrocytes with toxin-induced stellate morphology survive toxin treatment, the progression of cell morphology and cytoskeleton organization were followed for several weeks. Twenty-six days after exposure to toxin B, stellate astrocytes have processes which were markedly longer and much more branched than those of cells freshly exposed to toxin. At that time, cells are still devoid of F-actin as assessed with rhodamine-conjugated phalloidin and only 70% contain vimentin while all astrocytes present in control cultures express vimentin. Some flat epithelioid astrocytes with prominent bundles of microfilaments reappear during the second week after toxin treatment. Our results show that Clostridium difficile toxin B is internalized into brain astrocytes in culture where it acts by modifying cytoskeletal elements. Its cytopathic effects are reversible. Although actin-related components of the cytoskeleton are the major target of toxin B, other cytoskeletal elements also seem to be affected.     

Hsp90 and the quantitative variation of wing shape in Drosophila melanogaster

The molecular chaperone protein Hsp90 has been widely discussed as a candidate gene for developmental buffering. We used the methods of geometric morphometrics to analyze its effects on the variation among individuals and fluctuating asymmetry of wing shape in Drosophila melanogaster. Three different experimental approaches were used to reduce Hsp90 activity. In the first experiment, developing larvae were reared in food containing a specific inhibitor of Hsp90, geldanamycin, but neither individual variation nor fluctuating asymmetry was altered. Two further experiments generated lines of genetically identical flies carrying mutations of Hsp83, the gene encoding the Hsp90 protein, in heterozygous condition in nine different genetic backgrounds. The first of these, introducing entire chromosomes carrying either of two Hsp83 mutations, did not increase shape variation or asymmetry over a wild-type control in any of the nine genetic backgrounds. In contrast, the third experiment, in which one of these Hsp83 alleles was introgressed into the wild-type background that served as the control, induced an increase in both individual variation and fluctuating asymmetry within each of the nine genetic backgrounds. No effect of Hsp90 on the difference among lines was detected, pro,iding no evidence for cryptic genetic variation of wing shape. Overall, these results suggest that Hsp90 contributes to, but is not controlling, the buffering of phenotypic variation in wing shape.     

HLA Class I Subtype-Dependent Expansion of KIR3DS1+ and KIR3DL1+ NK Cells during Acute Human Immunodeficiency Virus Type 1 Infection

NK cells are critical in the early containment of viral infections. Epidemiological and functional studies have shown an important role of NK cells expressing specific killer immunoglobulin-like receptors (KIRs) in the control of human immunodeficiency virus type 1 (HIV-1) infection, but little is known about the mechanisms that determine the expansion of these antiviral NK cell populations during acute HIV-1 infection. Here we demonstrate that NK cells expressing the activating receptor KIR3DS1⁺ and, to a lesser extent, the inhibitory receptor KIR3DL1⁺ specifically expand in acute HIV-1 infection in the presence of HLA-B Bw480I, the putative HLA class I ligand for KIR3DL1/3DS1. These data demonstrate for the first time the HLA class I subtype-dependent expansion of specific KIR⁺ NK cells during an acute viral infection in humans.NK cells are cytotoxic effector cells that play a vital role in the innate immune response to viral infections (9, 12, 33). The critical role of NK cells in acute viral infections has been best characterized in acute murine cytomegalovirus (MCMV) infection (14, 28). While several murine lab strains are resistant to MCMV infection, others are highly susceptible. Resistance to MCMV infection was mapped to a gene encoding an activating NK cell receptor, Ly49H, which has been shown to be critical in the early recognition and control of MCMV infection via the direct recognition of a viral product (M157) expressed on infected cells (28). Remarkably, MCMV-infected mice exhibit a dramatic expansion of NK cells during acute infection, but this expansion is restricted to the specific accumulation of Ly49H⁺ NK cells (16). Data from these studies suggest that the antiviral activity of the Ly49H⁺ NK cells is linked to their ability to expand early in infection, prior to the development of adaptive antiviral immunity.While the critical role of Ly49H⁺ NK cells in MCMV infection has been well established, very little is known about the clonal composition of NK cells that expand in human viral infections, and the NK cell receptors that mediate their antiviral activity. Unlike T cells and B cells, the specificity of NK cells is not determined by a single NK cell receptor (8); rather, NK cells express an array of activating and inhibitory receptors that regulate their activity. While the expression of these receptors is stochastic, the random combinations of different receptors on the surface of a given NK cell clone determine its ability to respond to a specific target cell (26, 27). It has been suggested that individual NK cell populations expressing a specific array of receptors may respond differentially to diverse viral infections (7). This has been further supported by epidemiological studies associating the expression of individual activating or inhibitory NK cell receptors in combination with their HLA class I ligands with better or worse disease outcomes in viral infections such as hepatitis C virus (22), human immunodeficiency virus (HIV) (29, 30), human papillomavirus (11), and CMV (7). The functional basis for this protective immunity mediated by NK cells in human viral infections remains largely unknown.Similar to MCMV infection, highly functional NK cells expand rapidly in acute HIV-1 infection, prior to the induction of adaptive immune responses (2). One particular activating killer immunoglobulin-like NK cell receptor (KIR3DS1), in combination with its putative ligand, an HLA-B allele with isoleucine at position 80 (HLA-B Bw480I), has been shown to be associated with slower HIV-1 disease progression (29). We have recently shown that KIR3DS1⁺ NK cells can effectively suppress HIV-1 replication in HLA-B Bw480I⁺ target cells in vitro (1). Furthermore, a subset of inhibitory alleles from the same locus, KIR3DL1, that show high cell surface expression levels have similarly been associated with slower disease progression toward AIDS in the presence of their ligand, HLA-B Bw480I (30). These data suggest that both KIR3DS1⁺ and KIR3DL1⁺ NK cells may play a critical role in the control of natural HIV-1 infection, depending on the interaction with their ligand on infected cells (4). However, the mechanisms underlying their protective role are not understood.Given the critical role of NK cells in acute viral infections and the described expansion of NK cells overall during acute HIV-1 infection (16), we assessed clonal NK cell expansions during acute HIV-1 infection by quantitative PCR and flow cytometric analysis. Here we report an HLA class I subtype-dependent specific expansion of KIR3DS1⁺ and KIR3DL1⁺ NK cells during acute HIV-1 infection. These data demonstrate for the first time the impact of the HLA class I ligands on clonal NK cell expansions during an acute human viral infection.     

Extreme Genetic Fragility of the HIV-1 Capsid

Genetic robustness, or fragility, is defined as the ability, or lack thereof, of a biological entity to maintain function in the face of mutations. Viruses that replicate via RNA intermediates exhibit high mutation rates, and robustness should be particularly advantageous to them. The capsid (CA) domain of the HIV-1 Gag protein is under strong pressure to conserve functional roles in viral assembly, maturation, uncoating, and nuclear import. However, CA is also under strong immunological pressure to diversify. Therefore, it would be particularly advantageous for CA to evolve genetic robustness. To measure the genetic robustness of HIV-1 CA, we generated a library of single amino acid substitution mutants, encompassing almost half the residues in CA. Strikingly, we found HIV-1 CA to be the most genetically fragile protein that has been analyzed using such an approach, with 70% of mutations yielding replication-defective viruses. Although CA participates in several steps in HIV-1 replication, analysis of conditionally (temperature sensitive) and constitutively non-viable mutants revealed that the biological basis for its genetic fragility was primarily the need to coordinate the accurate and efficient assembly of mature virions. All mutations that exist in naturally occurring HIV-1 subtype B populations at a frequency >3%, and were also present in the mutant library, had fitness levels that were >40% of WT. However, a substantial fraction of mutations with high fitness did not occur in natural populations, suggesting another form of selection pressure limiting variation in vivo. Additionally, known protective CTL epitopes occurred preferentially in domains of the HIV-1 CA that were even more genetically fragile than HIV-1 CA as a whole. The extreme genetic fragility of HIV-1 CA may be one reason why cell-mediated immune responses to Gag correlate with better prognosis in HIV-1 infection, and suggests that CA is a good target for therapy and vaccination strategies.