Interleukin-10 promoter polymorphisms and the outcome of hepatitis C virus infection

The natural outcome and response to treatment in hepatitis C virus (HCV) infection varies between individuals. Whereas some variation may be attributable to viral and environmental variables, it is probable that host genetic background also plays a significant role. Interleukin (IL)-10 has a key function in the regulation of cellular immune responses and in the suppression of pro-inflammatory cytokine secretion. Functional polymorphisms in the IL-10 gene have been described. We investigated the role of these polymorphisms in the outcome of HCV infection, treatment response and development of fibrosis in a case-control association study. Self-limiting infection was associated with the IL-10 (–592) AA genotype (OR=2.05; P=0.028). Persistent infection was associated with the IL-10 (–1082) GG genotype (OR=0.48; P=0.018). Sustained response to interferon therapy was associated with the IL-10 (–1082) GG genotype (OR=2.28; P=0.005) and the haplotype GCC (OR=2.27; P=0.020). The IL-10 (–1082) AA genotype and the ATA/ATA and ACC/ACC homozygous haplotypes were more frequent among patients with rapid fibrosis. Furthermore, the microsatellites IL-10.R and IL-10.G were associated with interferon response with IL-10R.2 conveying susceptibility (OR=1.80; P=0.034), and IL-10R.3 and IL-10.G13 being protective (OR=0.47; P=0.003 and OR=0.59; P=0.042, respectively). We conclude that polymorphisms in the IL-10 promoter appear to have some influence on the outcome of HCV infection, treatment and development of fibrosis.Susanne Knapp and Branwen Hennig contributed equally to this study     

Detection of marker associations with a dominant disease gene in genetically complex and heterogeneous diseases.

Linkage disequilibrium of a marker allele with disease may characterize a chromosomal region containing the disease gene. In several diseases, only a limited number of pedigrees are linked to a particular region, because of linkage heterogeneity. Disequilibrium in this situation is more easily detected when the association is positive (an infrequent marker allele associated with disease mutation), and sampling is conditional on presence or absence of illness in individuals or gametes. Defining H as the marker frequency in illness-transmitting gametes, and Q the marker frequency in normal chromosomes, we compute the power of a given sample (of ill persons/gametes) to detect association in a disease that is genetically heterogeneous, with a dominantly transmitted form linked to a marker. The estimation of Q and the effects of linkage heterogeneity (when unrelated individuals are examined) are also analyzed. Two linked pedigrees give acceptable power to detect association when the allele is frequent enough in illness gametes (H greater than or equal to .6) and infrequent enough in normals (Q less than or equal to .01). If H greater than or equal to .2, 14 pedigrees are needed to give the same power. From the analysis of different values of Q and H, it appears that even in the presence of considerable genetic heterogeneity and complex inheritance (where some normals carry the disease mutation), association may be detected with clinically feasible sample sizes.     

Formation of unilamellar lipid vesicles of controllable dimensions by detergent dialysis.

Vesicles are formed by solubilizing mixtures of phosphatidylcholine and cholesterol with sodium cholate and removing the detergent by rapid (hollow fiber) dialysis [e.g., Goldin, S. M. (1977) J. Biol. Chem. 252, 5630--5642]. Characterization of the vesicle size distribution by agarose gel filtration, and determination of the intravesicular aqueous compartment, demonstrates that the vesicles are relatively homogeneous in size and are primarily unilamellar. The mean diameter of the vesicles can be varied from 340 to 1280 A by varying the conditions under which they are formed; increasing the mole fraction of cholesterol and lowering the pH of the dialysate tend to produce larger vesicles. The gentle detergent treatment required for vesicle formation and the ability to control vesicle size distribution reproducibly may make this method particularly useful in studies of reconstitution of membrane proteins and in use of vesicles as vehicles for delivery of materials to living cells.     

Biochemical and immunological evidence for a calcium pump in chromaffin granules

ATP stimulated the accumulation of 45Ca2+ by chromaffin granule ghosts which contained 5 mM oxalate to trap transported calcium within the lumen. Inasmuch as the ATP-dependent 45Ca2+ transport was resistant to 25 mM ammonium acetate as well as the proton ionophore, carbonylcyanide-m-chlorophenylhydrazone, the chromaffin granule proton translocating ATPase does not provide the energy for this process. Instead, we suggest that chromaffin granules contain a calcium translocating ATPase which catalyzes the 45Ca2+ uptake directly. The observation that chromaffin granules bind to a monoclonal antibody raised against a calcium pump from bovine brain supports this hypothesis.     

High throughput screening for small molecule therapy for Gaucher disease using patient tissue as the source of mutant glucocerebrosidase

Gaucher disease (GD), the most common lysosomal storage disorder, results from the inherited deficiency of the lysosomal enzyme glucocerebrosidase (GCase). Previously, wildtype GCase was used for high throughput screening (HTS) of large collections of compounds to identify small molecule chaperones that could be developed as new therapies for GD. However, the compounds identified from HTS usually showed reduced potency later in confirmatory cell-based assays. An alternate strategy is to perform HTS on mutant enzyme to identify different lead compounds, including those enhancing mutant enzyme activities. We developed a new screening assay using enzyme extract prepared from the spleen of a patient with Gaucher disease with genotype N370S/N370S. In tissue extracts, GCase is in a more native physiological environment, and is present with the native activator saposin C and other potential cofactors. Using this assay, we screened a library of 250,000 compounds and identified novel modulators of mutant GCase including 14 new lead inhibitors and 30 lead activators. The activities of some of the primary hits were confirmed in subsequent cell-based assays using patient-derived fibroblasts. These results suggest that primary screening assays using enzyme extracted from tissues is an alternative approach to identify high quality, physiologically relevant lead compounds for drug development.     

A genome‐wide CRISPR screen identifies FBXO42 involvement in resistance toward MEK inhibition in NRAS‐mutant melanoma

NRAS mutations are the most common alterations among RAS isoforms in cutaneous melanoma, with patients harboring these aggressive tumors having a poor prognosis and low survival rate. The main line of treatment for these patients is MAPK pathway‐targeted therapies, such as MEK inhibitors, but, unfortunately, the response to these inhibitors is variable due to tumor resistance. Identifying genetic modifiers involved in resistance toward MEK‐targeted therapy may assist in the development of new therapeutic strategies, enhancing treatment response and patient survival. Our whole‐genome CRISPR‐Cas9 knockout screen identified the target Kelch domain‐containing F‐Box protein 42 (FBXO42) as a factor involved in NRAS‐mutant melanoma‐acquired resistance to the MEK1/2 inhibitor trametinib. We further show that FBXO42, an E3 ubiquitin ligase, is involved in the TAK1 signaling pathway, possibly prompting an increase in active P38. In addition, we demonstrate that combining trametinib with the TAK1 inhibitor, takinib, is a far more efficient treatment than trametinib alone in NRAS‐mutant melanoma cells. Our findings thus show a new pathway involved in NRAS‐mutant melanoma resistance and provide new opportunities for novel therapeutic options.     

Mapping of the mucolipidosis type IV gene to chromosome 19p and definition of founder haplotypes.

Mucolipidosis type IV (MLIV) is a lysosomal storage disorder characterized by severe neurologic and ophthalmologic abnormalities. It is a rare autosomal recessive disease, and the majority of patients diagnosed, to date, are of Ashkenazi Jewish descent. We have mapped the MLIV gene to chromosome 19p13.2-13.3 by linkage analysis with 15 markers in 13 families. A maximum LOD score of 5.51 with no recombinants was observed with marker D19S873. Several markers in the linked interval also displayed significant linkage disequilibrium with the disorder. We constructed haplotypes in 26 Ashkenazi Jewish families and demonstrate the existence of two founder chromosomes in this population. The localization of MLIV to chromosome 19 will permit genetic prenatal diagnosis in affected families and will aid in the isolation of the disease gene.     

Topology of the Shaker Potassium Channel Probed with Hydrophilic Epitope Insertions

The structure of the Shaker potassium channel has been modeled as passing through the cellular membrane eight times with both the NH₂ and COOH termini on the cytoplasmic side (Durrell, S.R., and H.R. Guy. 1992. Biophys. J. 62:238–250). To test the validity of this model, we have inserted an epitope consisting of eight hydrophilic amino acids (DYKDDDDK) in predicted extracellular and intracellular loops throughout the channel. The channels containing the synthetic epitope were expressed in Xenopus oocytes, and function was examined by two-electrode voltage clamping. All of the mutants containing insertions in putative extracellular regions and the NH₂ and COOH termini expressed functional channels, and most of their electrophysiological properties were similar to those of the wild-type channel. Immunofluorescent staining with a monoclonal antibody against the epitope was used to determine the membrane localization of the insert in the channels. The data confirm and constrain the model for the transmembrane topology of the voltage-gated potassium channel.