Effect of siRNA terminal mismatches on TRBP and Dicer binding and silencing efficacy.

To enhance silencing and avoid off-target effects, siRNAs are often designed with an intentional bias to ensure that the end of the siRNA that contains the guide strand 5' end is less stably hybridized relative to the end containing the passenger strand 5' end. One means by which this is accomplished is to introduce a terminal mismatch, typically by changing the passenger strand sequence to impair its hybridization with the guide strand 5' end. However, there are conflicting reports about the influence of terminal mismatches on the silencing efficacy of siRNAs. Here, the silencing efficiency of siRNAs with a terminal mismatch generated either by altering the guide strand (at the 5' end, nucleotide 1) or the passenger strand (nucleotide 19 from the 5' end) was examined. Subsequently, we studied the relationship between the silencing efficiency of the siRNAs and their binding to the RNA-induced silencing complex loading complex proteins HIV transactivating response RNA-binding protein and Dicer in H1299 cytoplasmic extracts. Binding of siRNA and the transactivating response RNA-binding protein was significantly reduced by terminal mismatches, which largely agrees with the reduction in eventual silencing efficacy of the siRNAs. Single terminal mismatches led to a small increase in Dicer binding, as expected, but this did not lead to an improvement in silencing activity. These results demonstrate that introduction of mismatches to control siRNA asymmetry may not always improve target silencing, and that care should be taken when designing siRNAs using this technique.

Rational selection and quantitative evaluation of antisense oligonucleotides.

Antisense oligonucleotides are an attractive therapeutic option to modulate specific gene expression. However, not all antisense oligonucleotides are effective in inhibiting gene expression, and currently very few methods exist for selecting the few effective ones from all candidate oligonucleotides. The lack of quantitative methods to rapidly assess the efficacy of antisense oligonucleotides also contributes to the difficulty of discovering potent and specific antisense oligonucleotides. We have previously reported the development of a prediction algorithm for identifying high affinity antisense oligonucleotides based on mRNA-oligonucleotide hybridization. In this study, we report the antisense activity of these rationally selected oligonucleotides against three model target mRNAs (human lactate dehydrogenase A and B and rat gp130) in cell culture. The effectiveness of oligonucleotides was evaluated by a kinetic PCR technique, which allows quantitative evaluation of mRNA levels and thus provides a measure of antisense-mediated decreases in target mRNA, as occurs through RNase H recruitment. Antisense oligonucleotides that were predicted to have high affinity for their target proved effective in almost all cases, including tests against three different targets in two cell types with phosphodiester and phosphorothioate oligonucleotide chemistries. This approach may aid the development of antisense oligonucleotides for a variety of applications.

Coupling of inflammatory cytokine signaling pathways probed by measurements of extracellular acidification rate.

There is a growing interest in the mechanisms of how cells integrate the multitude of signals that emanate during inflammatory stimuli, such as the hepatic acute phase response to burn or trauma. We have used measurements of extracellular acidification rate (ECAR) of HepG2 cells cultured on microporous membranes to probe the coupling between signaling pathways for gp130 family cytokines (interleukin-6, oncostatin M) and IL-1, each of which is considered to play a significant role in the hepatic acute phase response. We found that brief (30 min or less) exposure to any of these cytokines desensitized the HepG2 cells to subsequent exposure with the same cytokine. Furthermore, we found that this property serves as a probe of the coupling of signaling pathways: exposure to IL-1 did not desensitize the cells to exposure to OSM and vice versa. However, cells exposed to IL-6 with soluble gp80, which together share with OSM the use of gp130 as a signal transducing receptor, were subsequently unable to respond to OSM, and vice versa. Simultaneous exposure of cells to moderate concentrations (near their respective EC50 values) of both IL-1 and OSM resulted in synergistic effects on the ECAR, but simultaneous exposure to saturating concentrations of IL-1 and OSM resulted in a response that tracked that of OSM alone. These results suggest that the signaling pathways of IL-1 and OSM may be simultaneously activated in HepG2 cells under moderate inflammatory cytokine challenge but that the cells must prioritize their response under extreme cytokine challenges.

Clinical significance of immunoassays for type-5 tartrate-resistant acid phosphatase.

BACKGROUND: Tartrate-resistant acid phosphatase (TRAP; EC 3.1.3.2) is a product of osteoclasts and a biochemical marker of bone resorption rate. However, erythrocytes and platelets contribute to total TRAP activity in serum, reducing the specificity of direct biochemical assays in serum. Osteoclast TRAP is also known as type-5 TRAP and is antigenically unique. Immunoassays are sought to improve the specificity and sensitivity of TRAP as a bone marker. METHODS: We developed two colorimetric microplate assays for type-5 TRAP: an enzyme capture immunoassay to measure antibody-bound enzymatic activity, and a two-site immunoassay to measure bound enzyme protein. Both use the same monoclonal antibody (14G6) to capture type-5 TRAP, which permits determination of specific activity of serum TRAP in health and disease. RESULTS: Both TRAP assays were linear from one-tenth to fivefold the mean value in 18 healthy subjects. In these subjects, the mean (SD) TRAP activity was 3.2 (0.54) U/L for the enzyme capture assay and 37 (13) microg/L for the two-site assay. Mean TRAP activity was not significantly increased in 64 patients with endstage renal disease requiring hemodialysis (HD) or 99 unselected patients with rheumatic diseases. By contrast, TRAP protein was increased in both the HD and rheumatic disease groups. The specific activity of TRAP in the 17 of 64 HD sera that had increased TRAP activity (0.088 U/microg) was similar to that in healthy subjects (0.091 U/microg). By contrast, the specific activity of TRAP in the 31 of 99 rheumatic sera with increased TRAP protein (0.035 U/microg) was significantly decreased. CONCLUSIONS: Wide sample distributions for TRAP activity in HD patients and TRAP protein in rheumatic disease patients suggest the presence of subpopulations of HD patients with increased TRAP activity and of rheumatic patients with increased TRAP protein. Each assay for TRAP activity and protein may have its own biological significance and clinical applications in specific groups of patients.

Prediction of antisense oligonucleotide binding affinity to a structured RNA target.

Antisense oligonucleotides, which act through the pairing of complementary bases to an RNA target sequence, are showing great promise in research and clinical applications. However, the selection of effective antisense oligonucleotides has proven more difficult than initially presumed. We developed a prediction algorithm to identify those sequences with the highest predicted binding affinity for their target mRNA based on a thermodynamic cycle that accounts for the energetics of structural alterations in both the target mRNA and the oligonucleotide. The model was used to predict the binding affinity of antisense oligonucleotides complementary to the rabbit beta-globin (RBG) and mouse tumor necrosis factor-alpha (TNFalpha) mRNAs, for which large experimental datasets were available. Of the top ten candidates identified by the algorithm for the RBG mRNA, six were the most strongly binding sequences determined from an experimental assay. The prediction for the TNFalpha mRNA also identified high affinity sequences with approximately 60% accuracy. Computational prediction of antisense efficacy is more cost-efficient and faster than in vitro or in vivo selection and can potentially speed the development of sequences for both research and clinical applications.

Species specificity of monoclonal antibodies to human tartrate-resistant acid phosphatase.

Tartrate-resistant acid phosphatase (TRAP) is expressed abundantly by osteoclasts and is required for bone resorption. This enzyme is emerging as an important biomarker in bone pathology, both for histochemical identification of osteoclasts and as a serum marker of osteoclast activity and increased bone turnover. Rat and mouse models are becoming popular systems for studying osteoclast development, bone physiology and morphogenesis, and bone diseases such as osteoporosis. We have developed two unique antibodies to human TRAP purified from hairy cell leukemia spleen. Both antibodies (9C5 and 14G6) are suitable for immunohistochemistry of osteoclasts and macrophages. Only one (14G6) is capable of immunoprecipitating active TRAP from human cell lysates. Antibody 9C5 reacts with a denatured epitope of TRAP while antibody 14G6 probably reacts with a native, conformational determinant. The high degree of homology among TRAPs of various species predicts that these antibodies should be suitable for work in experimental animals as well as humans. Immunohistochemical staining, electrophoretic analyses, immunoprecipitation and immunoblotting assays of human rat and mouse TRAP were carried out to test the validity of these antibodies as cell markers in rodents. Both antibodies were suitable for immunohistochemistry in all species. Antibody 9C5 was suitable for immunoblotting of denatured TRAP of all species tested. Antibody 14G6 reacted with the native TRAP of humans only and failed to immunoprecipitate mouse or rat TRAP activity. Although TRAP is a phylogenetically conserved protein, subtle, species-specific determinants exist. Care should be exercised when anti-TRAP antibodies are used for immunoassay in experimental animals.

Comparison of magnetic resonance imaging and Laser Doppler Anemometry velocity measurements downstream of replacement heart valves: implications for in vivo assessment of prosthetic valve function.

BACKGROUND AND AIM OF THE STUDY: The non-invasive, in-vivo assessment of prosthetic valve function is compromised by the lack of accurate measurements of the transvalvular flow fields or hemodynamics by current techniques. Short echo time magnetic resonance imaging (MRI) may provide a method for the non-invasive, in vivo assessment of prosthetic valve function by accurately measuring changes in the transvalvular flow fields associated with normal and dysfunctional prosthetic valves. The objectives of these in vitro experiments were to investigate the potential for using MRI as a tool to measure the complex flow fields distal to replacement heart valves, and to assess the accuracy of MRI velocity measurements by comparison with Laser Doppler Anemometry (LDA), a gold standard. METHODS: The velocity fields downstream of tilting disc, bileaflet, ball and cage, and pericardial tissue valves were measured using both three-component LDA and MRI phase velocity encoding under a steady flow rate of 22.8 l/min, simulating peak systolic flow. The valves were tested under normal and stenotic conditions to assess the MRI capabilities under a wide range of local flow conditions, velocities and turbulence levels. A new short echo time MRI technique (FAcE), which allowed velocity measurements in stenotic jets with high turbulence, was tested. RESULTS: Good overall agreement was obtained between the MRI velocity measurements and the LDA data. The MRI velocity measurements adequately reproduced the spatial structure of the flow fields. In most cases peak velocities were accurately measured to within 15%. CONCLUSIONS: The results indicate that the FAcE MRI method has the potential to be used as a diagnostic tool to assess prosthetic valve function.

Demonstration of antiphospholipid antibody heterogeneity by phospholipid column chromatography and salt gradient elution techniques.

Antiphospholipid (aPL) antibodies are associated with thrombosis, recurrent abortions and thrombocytopenia. Studies to determine the mechanisms of action of these antibodies have been hindered by their heterogeneity and limited availability of techniques to isolate and characterize subgroups of the antibodies. We report a new phospholipid affinity chromatography method which enables separation of antiphospholipid positive sera into more than one antibody subpopulation. Sera from five patients with complications of the antiphospholipid syndrome (APS) were studied. Each serum was applied to chromatography columns prepared by coating polystyrene beads (diameter 100 A) with phosphatidylserine (PS) or cardiolipin (CL). A linear salt gradient (0.03-1.0 M NaCl) was used for elution. Eluates were analyzed for phospholipid binding and for inhibition of the prothrombin-thrombin conversion reaction. Each sample yielded two to three peaks for CL and PS affinity columns. Molarities at which peaks were eluted differed between samples. For individual samples, molarities at which peaks were eluted differed between CL and PS columns. These data suggest that aPL antibodies are heterogenous, with differences existing between patients and even within single serum samples. Subpopulations differed in their avidities for CL and PS but generally all had prothrombinase inhibitory activity.

Magnetic resonance velocity imaging: a new method for prosthetic heart valve study.

The aim of this study was to compare different (long/short echo time, whole body/small bore scanner) magnetic resonance velocity measurement techniques and their applicability to the measurement of blood velocity downstream of prosthetic heart valves. In-vitro magnetic resonance velocity measurements were performed downstream of four normal and stenotic prosthetic heart valves (St. Jude Medical bileaflet, Monostrut tilting disc, Ionescu-Shiley Pericardial and Starr-Edwards caged-ball) under steady flow conditions in an aortic test chamber. Cross-sectional and longitudinal velocity images were obtained downstreamed of the valves. Magnetic resonance was able to measure all three components of fluid velocity downstream of the valves under normal and stenotic conditions except in regions of turbulence. The velocity was measured across the tube cross-section in 10-15 minutes producing a good visualization of the axial velocity profile. High velocity regions, shear layers and reversed/stagnant regions were identified. The flow rate calculated by integration of the magnetic resonance velocity across the cross-section of the tube was accurate to 5-6% in normal cases and slightly less accurate for stenotic valves. Although signal loss on the modulus image was adverse to the velocity images, it was found that these regions could be used to identify areas of flow disturbance. The high magnetic field, small bore scanner was able to produce images with a resolution of 0.2 x 0.2 x 1.0 mm and was less affected by turbulence producing more detailed flow images. Magnetic resonances has been shown to be a useful new tool in the measurement of the velocity downstream of prosthetic heart valves. In particular it's short data acquisition time and the possibilities to reproduce the same measurements in-vivo make it an attractive alternative to traditional methods.

Pulmonary fibrosis and occupational exposure to aluminum.

Many reports of respiratory disease attributable to aluminum exposure have appeared in the European medical literature during the last 50 years. Great Britain and Germany are two major industrialized nations that acknowledge a causal relationship between occupational exposure to aluminum and respiratory impairment. For factory workers in these countries, pulmonary disease attributed to respirable aluminum particulates is compensated as a workplace disability. In North America, however, there is a lack of consensus regarding the pathogenicity of aluminum fumes and dust to the worker. This view may be based on a difference in the types of industrial usage, the updated methods of aluminum processing in this country, or the benefits of a modern workplace. It has also been proposed that the development of aluminum-induced pulmonary disease may depend on a particular host factor that has not yet been identified. We describe a patient whom we believe developed severe respiratory compromise and irreversible pulmonary fibrosis from a lifetime of industrial aluminum exposure.