Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience

Modeling and simulation in computational neuroscience is currently a research enterprise to better understand neural systems. It is not yet directly applicable to the problems of patients with brain disease. To be used for clinical applications, there must not only be considerable progress in the field but also a concerted effort to use best practices in order to demonstrate model credibility to regulatory bodies, to clinics and hospitals, to doctors, and to patients. In doing this for neuroscience, we can learn lessons from long-standing practices in other areas of simulation (aircraft, computer chips), from software engineering, and from other biomedical disciplines. In this manuscript, we introduce some basic concepts that will be important in the development of credible clinical neuroscience models: reproducibility and replicability; verification and validation; model configuration; and procedures and processes for credible mechanistic multiscale modeling. We also discuss how garnering strong community involvement can promote model credibility. Finally, in addition to direct usage with patients, we note the potential for simulation usage in the area of Simulation-Based Medical Education, an area which to date has been primarily reliant on physical models (mannequins) and scenario-based simulations rather than on numerical simulations.

Engineering targeted in vivo drug delivery. I. The physiological and physicochemical principles governing opportunities and limitations

A physiologically based model is presented to aid prediction of the pharmacological benefits to be derived from the administration of a drug as a targeted drug-carrier combination. An improvement in the therapeutic index and an increase in the therapeutic availability are the primary benefits sought. A measure of the former is obtained from the value of the drug targeting index, a newly derived parameter. Both the drug targeting index and the therapeutic availability are directly calculable. The minimum information needed for approximating both parameters is the candidate drug's total-body clearance and some knowledge of the target site's anatomy and blood flow. Drugs with high total-body clearance values that are known to act at target tissues having effective blood flows that are small relative to the blood flow to the normal eliminating organs will benefit most from combination with an efficient, targeted carrier. Direct elimination of the drug at the target site or at the tissue where toxicity originates dramatically improves the drug targeting index value. The fraction of drug actually released from the carrier at both target and nontarget sites can radically affect index values. In some cases a 1% change in the fraction of the dose delivered to the target can result in a 50% change in the drug targeting index value. It is argued that most drugs already developed have a low potential to benefit from combination with a drug carrier. The approach allows one to distinguish clearly those drugs that can benefit from combination with targeted in vivo drug carriers from those drugs that cannot.

Lymphatic transport of liposome-encapsulated drugs following intraperitoneal administration - effect of lipid composition

Tumor cells often metastasize through lymphatic channels. It follows that localization of antitumor agents in the lymphatics may be therapeutically beneficial. This study determines the extent to which lipid composition controls lymphatic transport of a model compound ((14)C-sucrose) in liposomes following intraperitoneal administration in rats. All liposomes tested had mean diameters of approximately 0.2 µm. Liposomes were administerd to thoracic duct cannulated rats, and (14)C was quantified in thoracic lymph, several lymph nodes, blood, urine, and peritoneal wash. Changing liposome composition altered the rate of absorption of (14)C from the peritoneal cavity, stability in biological fluids, and the relative ability of liposomes to be retained by lymph nodes. Stability in biological fluids (plasma and lymph) appeared to be a reasonable predictor of observed lymph node recovery. Direct measures of lymph node level alone were poor measures of the ability of liposomes to function as prototypal lymphatic drug carriers. Neutral liposomes were better at reaching the general circulation following absorption from the peritoneal cavity.

The Effect of Regional Variations of the Trabecular Bone Properties on the Compressive Strength of Human Vertebral Bodies

Cancellous centrum is a major component of the vertebral body and significantly contributes to its structural strength and fracture risk. We hypothesized that the variability of cancellous bone properties in the centrum is associated with vertebral strength. Microcomputed tomography (micro-CT)-based gray level density (GLD), bone volume fraction (BV/TV), and finite element modulus (E) were examined for different regions of the trabecular centrum and correlated with vertebral body strength determined experimentally. Two sets of images in the cancellous centrum were digitally prepared from micro-CT images of eight human vertebral bodies (T10-L5). One set included a cubic volume (1 per vertebral centrum, n = 8) in which the largest amount of cancellous material from the centrum was included but all the shell materials were excluded. The other set included cylindrical volumes (6 per vertebral centrum, n = 48) from the anterior (4 regions: front, center, left, and right of the midline of vertebra) and the posterior (2 regions: left and right) regions of the centrum. Significant positive correlations of vertebral strength with GLD (r (2) = 0.57, p = 0.03) and E (r (2) = 0.63, p = 0.02) of the whole centrum and with GLD (r (2) = 0.65, p = 0.02), BV/TV (r (2) = 0.72, p = 0.01) and E (r (2) = 0.85, p = 0.001) of the central region of the vertebral centrum were found. Vertebral strength decreased with increasing coefficient of variation of GLD, BV/TV, and E calculated from subregions of the vertebral centrum. The values of GLD, BV/TV, and E in centrum were significantly smaller for the anterior region than for the posterior region. Overall, these findings supported the significant role of regional variability of centrum properties in determining the whole vertebral strength.

Simulating leukocyte-venule interactions--a novel agent-oriented approach

Leukocyte recruitment into sites of inflammation involves a complex cascade of molecular interactions between the leukocyte and the endothelial cells of the inflamed venule. This report proposes a novel agent-oriented approach for simulating leukocyte-venule interactions during inflammation. We focus on modeling and simulating the initial steps of rolling, activation, and firm adhesion of neutrophils on TNF-alpha-treated mouse cremaster muscle venules.

Modeling transport kinetics with StarLogo

StarLogo, an agent-based modeling and simulation platform, was used to simulate adsorption-mediated transcytosis of a molecule from the lumen side of a cell membrane to the abluminal extra-cellular fluid (ECF). The model contains small nondiffusible substrate molecules, transporters, and substrate-transporter agents. The "reaction" is a transporter combining with the substrate which then crosses the cell cytoplasm. The substrate that is deposited on the ECF side becomes the "product". Results showed characteristics consistent with Michaelis-Menten enzyme kinetics. The model can serve as an example of agent-based modeling and simulation.

Simulating in vitro epithelial morphogenesis in multiple environments

In vitro studies of epithelial cell morphogenesis have demonstrated the influence of environment composition and orientation in the development of multicellular epithelial structures such as tubules and cysts. We have constructed a low resolution, discrete event simulation model and report on its use to explore how experimentally observed morphogenetic phenomena under four growth conditions might be generated and controlled. We identified simulation attributes that may have in vitro counterparts. We studied how changes in the logic governing simulated epithelial cell behavior might cause abnormal growth. Simulation results support the importance of a polarized response to the environment to the generation of a normal epithelial phenotype and show how disruptions of tight mechanistic control lead to aberrant growth characteristics.

Vascular injuries of the upper extremity

Vascular injuries of the upper extremity represent approximately 30% to 50% of all peripheral vascular injuries. The majority of injuries are to the brachial artery, and 90% of injuries are due to penetrating trauma. Return of function is often related to concomitant injury to peripheral nerves. However, timely restoration of blood flow is essential to optimize outcome. The diagnosis is made by physical examination and limited Doppler ultrasonography. Arteriography may be helpful if there are multiple sites of injury. Anticoagulation with heparin should be given if not otherwise contraindicated. Revascularization should be completed within the critical ischemic time: 4 hours for proximate injuries and 12 hours for distal injuries. Revascularization methods include resection and primary repair or resection with an interposition graft. The sequence of repair of multiple injuries to the extremity begins with arterial revascularization followed by skeletal stabilization and nerve and tendon repair.

A forecasting approach to accelerate drug development

The clinical phase of drug development should be concluded sooner and at a lower cost if primarily only the pivotal and supportive studies were to be conducted. Such improved efficiency requires development of a decision support system that delivers five new capabilities: (i) it enables one to predict a result of a clinical study and to identify those studies that are expected to have an acceptable probability of success; (ii) it will allow one to optimally utilize available pharmacokinetic and pharmacodynamic (PK/PD) data and improve its predictive capability as more data become available; (iii) it will enable one to project useful population results, not just mean results; (iv) predictions will be accompanied by a measure of reliability; and (v) expected initial clinical results will be predictable from animal and related drug class data. With such a tool population targets could be specified very early in the drug development programme, challenged, and then rationally revised at each step during the development process. This report describes progress in developing and testing a clinical trials Forecaster, a prototype for such a system. The Forecaster generates estimates of the joint density for a population of combined PK/PD parameters. That population then serves as a surrogate for the population of individuals. When the resulting joint density is sampled, the obtained sets of parameters may be used to generate data that is statistically indistinguishable from the original experimental data. Such simulated data can be used to validate assumptions, and make inferences on specified population targets that are accompanied by a measure of prediction reliability. We demonstrate use of the forecaster by employing N = 22 PK/PD parameter sets for an orally administered analgesic.

Bootstrapping for pharmacokinetic models: visualization of predictive and parameter uncertainty

PURPOSE

We explore use of "bootstrapping" methods to obtain a measure of reliability of predictions made in part from fits of individual drug level data with a pharmacokinetic (PK) model, and to help clarify parameter identifiability for such models.

METHODS

Simulation studies use four sets (A-D) of drug concentration data obtained following a single oral dose. Each set is fit with a two compartment PK model, and the "bootstrap" is employed to examine the potential predictive variation in estimates of parameter sets. This yields an empirical distribution of plausible steady state (SS) drug concentration predictions that can be used to form a confidence interval for a prediction.

RESULTS

A distinct, narrow confidence region in parameter space is identified for subjects A and B. The bootstrapped sets have a relatively large coefficient of variation (CV) (35-90% for A), yet the corresponding SS drug levels are tightly clustered (CVs only 2-9%). The results for C and D are dramatically different. The CVs for both the parameters and predicted drug levels are larger by a factor of 5 and more. The results reveal that the original data for C and D, but not A and B, can be represented by at least two different PK model manifestations, yet only one provides reliable predictions.

CONCLUSIONS

The insights gained can facilitate making decisions about parameter identifiability. In particular, the results for C and D have important implications for the degree of implicit overparameterization that may exist in the PK model. In cases where the data support only a single model manifestation, the "bootstrap" method provides information needed to form a confidence interval for a prediction.

Validation of a decision support system for use in drug development: pharmacokinetic data

PURPOSE

Single dose pharmacokinetic data from several individuals can be used to predict the fraction of the population that is expected to be within a therapeutic range. Without having some measure of its reliability, however, that prediction is only likely to marginally influence critical drug development decision making. The system (Forecaster) described generates an approximate prediction interval that contains the original prediction and where, for example, the probability is approximately 85% that a similar prediction from a new set of data will also be within the range. The goal is to validate that the system functions as designed.

METHODS

The strategy requires having a Surrogate Population (SP), which is a large number (> or = 1500) of hypothetical individuals each represented by set of model parameter values having unique attributes. The SP is generated so that a sample taken from it will give data that is statistically indistinguishable from the available experimental data. The automated method for building the SP is described.

RESULTS

Validation studies using 300 independent samples document that for this example the SP can be used to make useful predictions, and that the approximate prediction interval functions as designed.

CONCLUSIONS

For the boundary conditions and assumptions specified, the Forecaster can make valid predictions of pharmacokinetic-based population targets that without a SP would not be possible. Finally, the approximate prediction interval does provide a useful measure of prediction reliability.

Non-peptide glycoprotein IIb/IIIa inhibitors. 17. Design and synthesis of orally active, long-acting non-peptide fibrinogen receptor antagonists

The synthesis and pharmacological evaluation of 5 (L-738, 167), a potent, selective non-peptide fibrinogen receptor antagonist is reported. Compound 5 inhibited the aggregation of human gel-filtered platelets with an IC50 value of 8 nM and was found to be > 33000-fold less effective at inhibiting the attachment of human endothelial cells to fibrinogen, fibronectin, and vitronectin than it was at inhibiting platelet aggregation. Ex vivo platelet aggregation was inhibited by > 85% 24 h after the oral administration of 5 to dogs at 100 micrograms/kg. The extended pharmacodynamic profile exhibited by 5 appears to be a consequence of its high-affinity binding to GPIIb/IIIa on circulating platelets and suggests that 5 is suitable for once-a-day dosing.

Sequence-independent inhibition of RNA transcription by DNA dumbbells and other decoys

DNA dumbbells are stable, short segments of double-stranded DNA with closed nucleotide loops on each end, conferring resistance to exonucleases. Dumbbells may be designed to interact with transcription factors in a sequence-specific manner. The internal based paired sequence of DNA dumbbells in this study contains the X-box, a positive regulatory motif found in all MHC class II DRA promoters. In electrophoretic mobility shift assays (EMSAs), dumbbells and other oligonucleotides ('decoys') with the core X-box sequence were found to compete with the native strand for binding to X-box binding proteins (including RFX1). However, only the X-box dumbbell was capable of forming detectable complexes with such proteins using EMSA. In a model cell system, dumbbells were tested for their ability to block RFX1VP16 activation of a plasmid containing multiple repeats of the X-box linked to the CAT gene. While it appeared that dumbbells could block this activation, the effect was non-specific. This and further evidence suggests an inhibition of transcription, most likely via an interaction with the general transcriptional machinery.

Measures of uncertainty of pharmacokinetic and pharmacodynamic parameter estimates: a new computerized algorithm

Numerous algorithms exist to fit data to nonlinear models of the type used in chemistry, pharmacology, physiology, etc. Most include modules that provide some measure of the reliability of the estimated model parameters. The variance-covariance matrix (VCM) is the common tabulation of information that is used to quantify the parameter uncertainty as well as correlations between parameters. The VCM has its mathematical foundation in the linear regression world, where the dependent variable is a linear function of the parameters. However, when the model is not linear in its parameters, then the VCM is no longer an absolute quantitative measure of reliability of the parameter estimates and should be interpreted with caution. If the goal is to obtain a realistic and quantitative rather than a qualitative measurement of the parameter reliability, then it is necessary to have an alternative approach to describe the parameter likelihood region. We present a computerized algorithm that fills that need, and we compare its performance with the traditional VCM approach for different data sets. We also discuss criteria that may be used to determine when the VCM approach should and should not be used.

An oligonucleotide blocks interferon-gamma signal transduction

Interferon (IFN)-gamma is an important mediator of transplant graft rejection. It induces endothelial cell expression of HLA-DR and intercellular adhesion molecule-1, which render transplant grafts more susceptible to rejection by the host. Oligonucleotide 5'-GGG GTT GGT TGT GTT GGG TGT TGT GT-RNH2 (oligo I) blocks multiple IFN-gamma effects in human K562 cell cultures. A systematic approach revealed that oligo I has a novel, and potentially important, mode of action--it blocks the binding of IFN-gamma to its receptor, thus preventing activation of the IFN-gamma signal transduction pathway. The results are consistent with an aptamer mechanism of action, because oligo I exerts its inhibitory effects by interacting with protein, not intracellular nucleic acid targets, such as mRNA or genomic DNA.

PSD-95 is associated with the postsynaptic density and not with the presynaptic membrane at forebrain synapses

PSD-95, a prominent protein component of the postsynaptic density (PSD) fraction from rat forebrain, has been localized by light microscopy to dendrites of hippocampal neurons (Cho et al., 1992) and to the presynaptic plexus of cerebellar basket cells (Kistner et al., 1993). Here we extend these studies to show that an affinity-purified antibody to PSD-95 labels the dendrites of most neurons in the forebrain and of a subset of neurons in the cerebellum. To confirm that PSD-95 is associated with the PSD at forebrain synapses and to clarify whether it is also associated with the presynaptic membrane, we employed immunogold electron microscopy of forebrain synaptosomes. Gold-labeled antibodies to PSD-95 labeled postsynaptic densities in both intact and lysed forebrain synaptosomes but did not label presynaptic terminals or the presynaptic membrane. The asymmetric distribution of PSD-95 at synapses contrasts with that of its homologs, disks-large and ZO-1, which are arranged symmetrically at septate and tight junctions, respectively.

Screening and characterization of estrogenic activity from a hydroxystilbene library

BACKGROUND

Compounds that either inhibit or induce an estrogen response in vivo are important as potential drugs and biochemical tools. Non-steroidal stilbene analogs such as tamoxifen are known to function as both estrogen agonists and antagonists depending upon the analog structure. This family of compounds is amenable to parallel-manifold synthesis because stilbene analogs are easily synthesized using a single-step olefination reaction.

RESULTS

We have prepared a small 23-component hydroxystilbene library using a solid phase synthesis approach. The library was screened for estrogenic and antiestrogenic activity using a cell-based bioassay that measures estrogen receptor-mediated transcription of a reporter gene. Three of the analogs proved to have dose-dependent estrogenic activity with EC50 values between 5 microM and 15 microM. Further characterization of the hydroxystilbene-mediated estrogenic activity suggests that the agonist activity results from direct binding to the steroid site on the estrogen receptor with IC50 values of 1-10 microM.

CONCLUSIONS

The results of this study show that classic olefination chemistry can be adapted to a solid-phase format for parallel synthesis of analog libraries. Although yields varied for the individual analogs, sufficient quantity of pure material was obtained directly from the resin for structural characterization and biological evaluation. This study further validates solid-phase organic synthesis as a useful approach for rapid parallel-manifold library synthesis to augment both lead compound discovery and optimization.

Suppression of interferon-gamma induction of MHC class II and ICAM-1 by a 26-base oligonucleotide composed of deoxyguanosine and deoxythymidine

Interferon-gamma (IFN-gamma) is an important cytokine released by T lymphocytes and natural killer cells which is able to induce expression of class II MHC and ICAM-1, crucial factors in cellular immune response. HeLa S3, HS 27, and NF-71-1 are cell lines which can be induced to express HLA-DR and HLA-DP by exposure to IFN-gamma. When T2 (5'GGGGTTGGTTGTGTTGGGTGTTGTGTRNH(2)3') oligonucleotide was added at 5-20 microM every other day, cell surface induction of HLA-DR and HLA-DP by IFN-gamma was suppressed in a dose-dependent manner in HeLa S3. T2 suppressive effect on HLA class II was also observed in four different nontransformed human cell lines, HS 27 at passage 18, NF-71-1 at passage 5, human corneal endothelial cell at passage 5, and human retinal pigmented epithelial cell at passage 3. Control oligonucleotides had no suppressive effect. Northern hybridization showed that HLA-DR A mRNA induction by IFN-gamma was blocked by T2 in HeLa S3 and fibroblast 143B. The suppressive effect of T2 was also reversible as continued culture of the treated cells without further addition of the oligonucleotide allowed full re-expression of HLA-DR. Further experiments showed that T2 oligonucleotide was also able to inhibit IFN-gamma enhancement of ICAM-1 (CD54) on human corneal endothelial cell and human retinal pigmented epithelial cell. We conclude that T2 oligonucleotide is effective at suppressing HLA-DR, HLA-DP and ICAM-1 induction by IFN-gamma in transformed and nontransformed cells in vitro.

Inhibition of transcription factor binding to the HER2 promoter by triplex-forming oligodeoxyribonucleotides

We have identified a 28-bp homopurine/homopyrimidine sequence capable of triple helix (triplex) formation with G+T-rich oligodeoxyribonucleotides (oligos) within the critical proximal promoter of the HER2/neu/c-erbB2 (HER2) proto-oncogene. To investigate the possible therapeutic potential of triplex-forming oligos in HER2 overexpressing breast cancers, we have studied the ability of triplex formation to compete with and to inhibit the binding of a transcription factor to its consensus sequence at an adjacent site. Competition binding assays demonstrate that a triplex-forming oligo can inhibit transcription factor binding in a sequence-specific manner. Moreover, we find that the addition of both nucleotide and non-nucleotide 'tails' to triplex-forming oligos do not confer any enhancement of binding affinity, but provide additional inhibition of transcription factor binding, potentially by steric hindrance.

Paradoxical production of target protein using antisense RNA expression vectors

We used antisense RNA in a protocol designed to reduce estrogen receptor (ER) content in human breast cancer cells and observed paradoxical increases in ER levels. ER protein activity was measured using a highly sensitive reporter gene assay that relies on the ability of functional ER to bind a consensus estrogen response element (ERE) and drive the production of chloramphenicol acetyl-transferase (CAT). Upon transient transfection of ER-positive cell lines with three different vectors containing the full-length ER cDNA cloned in an antisense orientation, we observed unexpected increases in ER-driven CAT activity. To further investigate this phenomenon, expression from the antisense ER vectors was studied in an ER-negative breast tumor cell line, MDA-MB-453. ER activity was observed in these ER-negative cells upon transient transfection with each of three antisense ER vectors, but not from control vectors. Expression of ER from antisense constructs was 30-100-times less efficient than ER expression from isogenic sense constructs. The paradoxical ER activity was consistent with expected ER behavior in that it exhibited characteristic binding to the natural ligand, 17 beta-estradiol (E2), and it was inhibited by the antiestrogens, 4-hydroxy-tamoxifen (OHT) and ICI 164384 (ICI). Control vectors containing a truncated antisense ER cDNA produced no ER activity. Although the mechanism for this ER expression has not been determined, it appears likely that it is due to transcription off the opposite strand of the antisense construct.(ABSTRACT TRUNCATED AT 250 WORDS)

Characterization of the oligodeoxynucleotide-mediated inhibition of interferon-gamma-induced major histocompatibility complex class I and intercellular adhesion molecule-1

The major histocompatibility complex (MHC) Class I and II genes and intercellular adhesion molecule-1 (ICAM-1) are regulated by interferon-gamma in a variety of cell types. We have previously shown that the oligodeoxynucleotide 5'-GGG GTT GGT TGT GTT GGG TGT TGT GT-RNH2 (oligo I) inhibits the interferon-gamma-mediated enhancement of MHC Class I and ICAM-1 proteins in the K562 cell line. We have now investigated the mechanism of action of oligo I and report that it acts by inhibiting the binding of interferon-gamma to cells. We also show that the dose-response curves, the selectivity profile, and the kinetics of oligo I are consistent with this novel mechanism of action. The dose-response curves for oligo I, obtained using antibodies against the MHC Class I heavy chain, beta 2-microglobulin, or ICAM-1, are almost superimposable at each observation time. MHC Class I induction by 6400 units/ml interferon-alpha or interferon-beta or ICAM-1 enhancement by 800 units/ml tumor necrosis factor-alpha is not inhibited by oligo I. However, the synergistic induction of MHC Class I by mixtures of tumor necrosis factor-alpha and interferon-gamma is inhibited. Oligo I belongs to a class of active oligodeoxynucleotides that inhibits interferon-gamma-induced MHC Class I and ICAM-1 in K562 cells. The activity and potency is sequence-dependent, but remarkably different sequences can have comparable effects. The activity of oligo I in the HeLa S3 cell line inhibits the interferon-gamma-mediated enhancement of both ICAM-1 and MHC Class II DR and the interferon-gamma-mediated reduction in transferrin receptor expression. Thus, oligo I appears to specifically inhibit interferon-gamma-induced changes in protein expression, which is consistent with oligo I acting at an early step(s) in the induction process. Taken together, our results show that oligo I exerts its effects by inhibiting the association of interferon-gamma with the cell surface, which is a novel mechanism of action for oligodeoxynucleotides.

Characterization of apocytochrome C binding to human erythrocytes

The binding of 125I-labeled apocytochrome c to human erythrocytes was determined for free apocytochrome c concentrations at 10(-10)-10(-6) M. At about 2 x 10(-9) M, maximum cell association of apocytochrome c occurs at 50 mM NaCl and at 22 degrees C. Intact erythrocytes at 22 degrees C have three classes of apocytochrome c binding sites: one high-affinity noncooperative site (n1 = 728 per cell, Kd1 = 1.5 x 10(-9) M) and two positively cooperative sites (n2 = 3.7 x 10(4) per cell, Kd2 = 1.2 x 10(-7) M, alpha 2 = 2.0, and n3 = 2.5 x 10(5) per cell, Kd3 = 7.1 x 10(-7) M, alpha 3 = 12). Erythrocytes at 37 degrees C, and erythrocyte ghosts at 22 degrees C, also have three classes of apocytochrome c binding sites, and most sites are positively cooperative.

Calcium dependent cellular uptake of a c-myc antisense oligonucleotide

Because a major limitation of ODN (oligodeoxynucleotide) use is inefficient cellular uptake, methods to improve ODN uptake could have important implications in the investigational and possibly therapeutic use of ODNs. In this study, antisense c-myc ODN cellular uptake in elevated extracellular calcium was increased up to 48-fold in the four cell lines examined. The role of calcium in ODN cellular uptake was examined using a 21-base ODN complementary to the c-myc proto-oncogene and the Rauscher cells. Cells were pretreated with uptake inhibitors in either 1.8 (physiologic) or 5.4 mM calcium prior to addition of (32P) labelled ODN. In physiologic calcium conditions, ODN cellular uptake was partially dependent on cellular energy and a trypsin-sensitive surface protein. In contrast, in the presence of elevated (5.4 mM) extracellular calcium, trypsinization and metabolic inhibition had a reduced and no effect, respectively, on uptake. Endocytosis and lysosomotropic inhibitors did not decrease uptake in either calcium concentrations. Therefore, the mechanism of ODN uptake may depend on the level of extracellular calcium. Furthermore, surface binding accounted for approximately 60% of total uptake in both physiologic and elevated calcium concentrations, suggesting that the increased uptake was not due exclusively to increased surface binding. Thus, the predominant mechanism of ODN uptake may depend on the extracellular calcium concentration.

In vivo generation of highly abundant sequence-specific oligonucleotides for antisense and triplex gene regulation

Antisense and triplex oligonucleotides continue to demonstrate potential as mediators of gene-specific repression of protein synthesis. However, inefficient and heterogeneous cellular uptake, intracellular sequestration, and rapid intracellular and extracellular degradation represent obstacles to their eventual clinical utility. Efficient cellular delivery of targeted ribozymes can present similar problems. In this report we describe a system for circumventing these obstacles and producing large quantities of short, sequence-specific RNA oligonucleotides for use in these gene regulation strategies. The oligonucleotides are generated from a vector containing promoter, capping, and termination sequences from the human small nuclear U6 gene, surrounding a synthetic sequence incorporating the oligonucleotide of interest. In vivo, these oligonucleotides are produced constitutively and without cell type specificity in levels up to 5 x 10(6) copies per cell, reach steady-state levels of expression within 9 hours post-transfection, and are still readily detectable 7 days post-transfection. In addition, these oligonucleotides are retained in the nucleus, obtain a 5' gamma-monomethyl phosphate cap, and have an intracellular half-life of approximately one hour. This expression vector provides a novel and efficient method of intracellular delivery of antisense or triplex RNA oligonucleotides (and/or ribozymes) for gene regulation, as well as a cost-effective means of comparing the biological activity arising from a variety of different potential oligonucleotide sequences.

Detection of triplex-forming RNA oligonucleotides by triplex blotting

Triplex formation with RNA oligonucleotides and double-stranded (ds) DNA may provide a means of controlling gene expression from specific promoters and/or creating more selective DNA cleaving agents. We report the development of a novel technique, called triplex blotting, designed to detect RNA species capable of triplex formation with radiolabeled dsDNA probes within a background of total cellular RNA. Triplex blotting offers a new approach for screening potential RNA sequences for triplex formation with dsDNA targets, for comparing relative binding affinities of various triplex-forming RNAs and for confirming the specificity of triplex formation of a DNA target probe within total cellular RNA. In addition, the technique allows for repeated probing of the same filter while varying critical hybridization conditions such as pH, temperature or ionic strength.

Biological availability and nuclease resistance extend the in vitro activity of a phosphorothioate-3'hydroxypropylamine oligonucleotide

Augmented biological activity in vitro has been demonstrated in oligonucleotides (oligos) modified to provide nuclease resistance, to enhance cellular uptake or to increase target affinity. How chemical modification affects the duration of effect of an oligo with potent activity has not been investigated directly. We postulated that modification with internucleotide phosphorothioates and 3' alkylamine provided additional nuclease protection which could significantly extend the biological activity of a 26 mer, (T2). We showed this analog, sT2a, could maximally inhibit interferon gamma-induced HLA-DR mRNA synthesis and surface expression in both HeLa and retinal pigmented epithelial cells and could continue to be effective, in the absence of oligo, 15 days following initial oligo treatment; an effect not observed with its 3'amine counterpart, T2a. In vitro stability studies confirmed that sT2a conferred the greatest stability to nucleases and that cellular accumulation of 32P-sT2a in both cell types was also greater than other T2 oligos. Using confocal microscopy, we revealed that the intracellular distribution of sT2a favored greater nuclear accumulation and release of oligo from cytoplasmic vesicles; a pattern not observed with T2a. These results suggest that phosphorothioate-3'amine modification could increase the duration of effect of T2 oligo by altering nuclease resistance as well as intracellular accumulation and distribution; factors known to affect biological availability.

Inhibition of interferon-gamma-mediated immune functions by oligonucleotides. Suppression of human T cell proliferation by downregulation of IFN-gamma-induced ICAM-1 and Fc-receptor on accessory cells

Recent progress in gene therapy may provide a new strategy for prevention of allograft rejection. Oligonucleotides have been shown to inhibit specific gene transcription in both cell-free and living-cell systems. In our previous studies, a 26-mer oligonucleotide (T2) designed to form a triple helix with the X/X2 box promoter region of human MHC class II (DRA) gene was shown to prevent the induction by IFN-gamma of HLA-DR molecules. Here, we show that this oligonucleotide downregulates two other IFN gamma-inducible molecules, the adhesion molecule ICAM-1 and the Fc receptor for IgG on the surface of human cells. T2 has no effect on TNF alpha- and IL-1-mediated ICAM-1 upregulation, showing its specificity for IFN gamma. T2 oligonucleotide is shown to inhibit IFN gamma-mediated induction of Fc receptor on human blood monocytes as assessed by flow cytometry. Furthermore, pretreatment of monocytes with T2 resulted in suppression of anti-CD3-mediated peripheral blood T cell proliferation. The presented data suggest that oligonucleotide T2 blockade of IFN gamma-induction of different immune receptors on accessory cells is associated with inhibition of T cell proliferative responses.

Inhibition of interferon-gamma-induced major histocompatibility complex class I expression by certain oligodeoxynucleotides

We report that certain oligonucleotides are capable of inhibiting cell surface induction of the major histocompatibility complex class I (MHC-I) proteins by interferon-gamma in K562 cells. The inhibition by oligodeoxy-nucleotide I 5' GGG GTT GGT TGT GTT GGG TGT TGT GT-RNH2 is dose-dependent, with an EC50 24 hr after dosing of approximately 4 microM for 800 U/ml interferon-gamma. The reverse complement II 5' AC ACA ACA CCC AAC ACA ACC AAC CCC-RNH2 did not show activity. Oligodeoxynucleotide I inhibits induction of MHC-I by interferon-gamma, but does not inhibit induction by either interferon-alpha or interferon-beta. Four other oligodeoxynucleotides were also evaluated, and three showed activity against interferon-gamma at 25 microM.

3-substituted thieno[2,3-b][1,4]thiazine-6-sulfonamides. A novel class of topically active carbonic anhydrase inhibitors

3-Aminoalkyl derivatives of thieno[2,3-b][1,4]thiazine-6-sulfonamide were prepared for evaluation as topically active ocular hypotensive agents. The compounds described were found to be excellent in vitro inhibitors of carbonic anhydrase II and in vivo to lower intraocular pressure in three rabbit models of ocular hypertension. Compounds 20A, 20B, and 20C met the requirement of formulation as a 1% solution at pH 5.2, but none of the compounds described exhibited greater activity in the normotensive albino rabbit, the alpha-chymotrypsin-treated albino rabbit, or the normotensive pigmented rabbit than MK-927 or MK-507, the present clinical candidates.

Antisense c-myc oligonucleotide cellular uptake and activity

Previously described cell membrane transport mechanisms are unable to account completely for oligodeoxynucleotide cellular uptake. These charged macromolecules enter cells by an incompletely defined mechanism and downregulate gene expression in either the cytoplasm or nucleus. Thus, the goal of this research was to study the mechanism of phosphodiester oligonucleotide cellular uptake in Rauscher Red 5-1.5 erythroleukemia cells. An antisense c-myc oligodeoxynucleotide (21 bases) demonstrated biological activity in these cells using two types of proliferation assays and Northern blot analysis, and was internalized as visualized by confocal laser microscopy. Oligonucleotide uptake appeared to be a complex process consisting of surface binding and internalization. Cellular internalization accounted for up to 40% of total uptake and was partially dependent on both a trypsin-sensitive component and cellular energy. Uptake in these cells was nonspecific and did not appear to be due to receptor-mediated endocytosis. Therefore, because oligonucleotide cellular uptake in other cell types apparently involves an endocytic mechanism, the primary mechanism of oligonucleotide internalization may be cell line dependent.

Characteristics of oligonucleotide uptake in human keratinocyte cultures

Oligodeoxyribonucleotides have the potential to interfere selectively with cellular protein synthesis by sequence-specific hybridization to DNA or RNA molecules. We have investigated the properties of uptake and intracellular localization of fluorescently labeled oligonucleotides in cultured human keratinocytes using confocal laser scanning microscopy. Unlike many other cell types studied, keratinocytes can internalize oligonucleotides without apparent sequestration in endosomes or cell surface accumulation. Uptake is primarily nuclear and unaltered by sodium azide, monensin, or chloroquine pretreatment. We have verified our results with two different fluorophores, fluorescein and Bodipy, and found similar uptake and distribution patterns in both live and fixed cell populations. Surprisingly, we have found uptake to be heterogeneous within a population, with 15-30% of cells internalizing the oligonucleotides. This percentage is drastically increased to roughly 80% at cell population margins, and after release from M phase arrest. These results on uptake and intracellular localization suggest that keratinocytes may have increased sensitivity as target cells for oligonucleotide based gene regulation strategies.

Predictions of effect for intracellular antisense oligodeoxyribonucleotides from a kinetic model

We have analyzed the implications of a simple two-compartment mathematical model (Hargrove and Schmidt, 1989) to anticipate the limits of antisense oligodeoxyribonucleotide action within single cells. The steady-state equations are derived for four special cases representing the following mechanisms: (i) ribosome blockage, (ii) mRNA cleavage by RNase H, (iii) concurrent ribosome exclusion and RNase H action, and (iv) decreased delivery of mature mRNA to the cytoplasm due to transcriptional blockage, interference with nucleocytoplasmic transport, or splicing. Dose-response relationships have been derived for these mechanisms under ideal conditions. Our results indicate that frequently translated mRNAs producing stable proteins are the most attractive antisense targets because these protein levels are sensitive to the changes in the mRNA levels that can be effected using antisense oligodeoxyribonucleotides. The nonsteady-state solutions show that both mRNA and protein half-life can determine the kinetics of antisense oligonucleotide action. A rapid onset of effect will be observed when the mRNA is rapidly degraded and slowly translated and when the translated protein is rapidly degraded. When the protein is slowly degraded, the kinetics of effect are limited by protein half-life. When the translational rate constant is large compared to the absolute difference between the mRNA and protein degradation rate constants, the kinetics of antisense action are determined by both degradation rate constants but are limited by the slower of the two degradative processes. We also show that the steady-state and nonsteady-state solutions may be used to design experiments that discriminate among mechanisms of antisense action.

The rat brain postsynaptic density fraction contains a homolog of the Drosophila discs-large tumor suppressor protein

In CNS synapses, the synaptic junctional complex with associated postsynaptic density is presumed to contain proteins responsible for adhesion between pre- and postsynaptic membranes and for postsynaptic signal transduction. We have found that a prominent, brain-specific protein (PSD-95) enriched in the postsynaptic density fraction from rat brain is highly similar to the Drosophila lethal(1)discs-large-1 (dlg) tumor suppressor protein. The dlg protein is associated with septate junctions in developing flies and contains a guanylate kinase domain that is required for normal control of cell division. The sequence similarity between dlg and PSD-95 suggests that molecular mechanisms critical for growth control in developing organisms may also regulate synapse formation, stabilization, or function in the adult brain.

Antisense c-myc oligodeoxyribonucleotide cellular uptake

Antisense oligonucleotides have therapeutic potential as inhibitors of gene expression. However, the mechanism by which an intact oligonucleotide reaches the intracellular site of action is unknown. In this study, we use an oligodeoxyribonucleotide 21-mer complementary to the translation initiation codon of the c-myc protooncogene to study the mechanism of oligonucleotide uptake and internalization into Rauscher Red 5-1.5 cells. We find trypsin-sensitive and trypsin-insensitive surface binding, in addition to internalization. Uptake is partially energy dependent and inhibited by charged molecules, including DNA, ATP, a random sequence oligonucleotide, and dextran sulfate. Uptake does not appear to occur via a traditional receptor-mediated uptake pathway because chloroquine, monensin, and phenylarsine oxide pretreatment does not significantly decrease internalization. An anion channel inhibitor, SITS, and the salts, NaCl, Na2SO4, and NH4Cl, significantly decrease oligonucleotide uptake. Whether uptake occurs via a channel or a novel uptake mechanism is still unknown. A model is proposed which reasonably simulates the experimental data.

Characterization and minimization of cellular autofluorescence in the study of oligonucleotide uptake using confocal microscopy

Intrinsic autofluorescent signals can interfere with extrinsic fluorophore signals when living cells are viewed under a confocal laser scanning microscope. The general pattern of this endogenous fluorescence is initially diffuse and cytoplasmic, but it can redistribute and intensify to become punctate and perinuclear as cells age. To reduce the contribution of autofluorescence when tracking the location of an extrinsic fluorophore, such as a fluorescently-labeled oligonucleotide, laser power settings, aperture settings, laser scanning rates, pH buffering environments, and excitatory wavelengths can be modulated. Decreasing laser power settings and aperture sizes, increasing laser scanning rates and excitatory wavelengths, and surrounding cells in a pH buffer all act to delay the signal transformation. In addition, the presence of an exogenous fluorophore can hasten the autofluorescent redistribution and intensification when compared to similar untreated cells.

Involvement in medical informatics may enable pharmacists to expand their consultation potential and improve the quality of healthcare

The outlook for pharmacy-related services foretells more involvement of both computers and information systems. Expert therapeutic systems and databases will enable pharmacists to expand their consultation potential through networks and improve the quality of healthcare that they provide. Therapeutic information management could be the largest pharmacy specialty of the future. As knowledge-based systems and networks become commonplace, there will be an increasing need for new components, system monitoring, and quality assurance. This is an opportunity for pharmacy to bring medical computing, as it relates to therapeutics, into the mainstream of the profession as a new discipline.

Buffer effects on swelling kinetics in polybasic gels

The swelling kinetics of polybasic gels consisting of copolymers of methyl methacrylate and dimethylaminoethyl methacrylate are studied in solutions at various acidic pH values, with monoacidic derivatives of acetic acid added as buffers. The effects of solution pH, as well as buffer pKa and concentration, on swelling rate are assessed. Gel swelling rate shows a nearly linear dependence on the concentration of nonionized buffer in the solution, as determined by the Henderson-Hasselbach equation. This result is explained in terms of the increased availability of protons that are carried by the nonionized buffer to bare amines on the gel. In fact, the so-called pH sensitivity of these gels, under these conditions, can be attributed mainly to the effect of pH on the nonionized buffer concentration. A practical consequence is that these gels may not reliably mediate pH-sensitive swelling-controlled release in oral applications, since the levels of buffer acids in the stomach (where swelling and release are expected to occur) generally cannot be controlled. However, the gels may be useful as mediators of pH-triggered release when precise rate control is of secondary importance.

Comparison and critique of two models for regional drug delivery

A simple stochastic recirculatory formalism is used to compare models of regional drug delivery due to Hunt et al. and Boddy and Aarons. It is shown that these two models are equivalent when regional delivery is ideal. The latter model has the advantage of simplicity. However, the former model appears more useful in relating predictions to experimentally accessible quantities. Neither model is sufficiently general to cover all possible topologies of regions associated with drug response and toxicity. Knowledge of this topology is essential in determining the drug targeting index. The underlying assumptions of the models are discussed, and situations where these assumptions may break down are identified. Finally, it is noted that the analysis of regional delivery may also apply to metabolite and prodrug kinetics.

Distribution and density of GABA cells in intralaminar and adjacent nuclei of monkey thalamus

The density of GABA-immunoreactive neurons was examined in the intralaminar and certain principal relay nuclei of the macaque monkey thalamus. Counts were made in 10-microns-thick frozen sections and in 1-micron-thick plastic sections and stereological formulae applied to obtain an accurate assessment of the volumetric density of GABA cells in the nuclei. It was found that GABA-immunoreactive cells account for at least 27% of the cells per unit area of all the thalamic nuclei investigated and up to as much as 50% by unit volume. The intralaminar nuclei show only slightly fewer GABA cells than the principal relay nuclei. Previous reports of their absence or relatively low numbers in the intralaminar nuclei probably stem from their smaller size, relatively weaker immunoreactive staining and from failure to apply stereometric formulae that reveal the density of neurons per volume of tissue. These results suggest that the cellular elements of the intralaminar nuclei are not fundamentally different from those of the principal relay nuclei of the thalamus.

Artificial red cells. A link between the membrane skeleton and RES detectability?

Factors governing nonspecific reticuloendothelial system (RES)-detectability are largely unknown. Will a liposome that mimics the lipid composition of the outer leaflet of the erythrocyte membrane be invisible to the RES? On both experimental and theoretical grounds we believe the answer is no, in part because 1) sorption of proteins is believed to be important in determining RES uptake, 2) a membrane skeleton is apparently necessary to inhibit protein sorption into erythrocyte membranes and 3) Neohemocytes (a liposome encapsulated hemoglobin product) currently lack a membrane skeleton. Neohemocytes with erythrocyte outer leaflet lipid composition do have extended circulation half-times, but these are at least two orders of magnitude shorter than the circulation half-times of erythrocytes. How might a membrane skeleton modulate RES-detectability? Can avoidance of opsonization result in part from the properties of the membrane skeleton? If so, then how? To explore and quantify such questions we have developed a theoretical, statistical-thermodynamic model of protein binding into membranes. It predicts that the membrane area available for rapid lateral diffusion is critically important in controlling the amount of sorbed protein per unit area, and that a membrane skeleton can reduce a protein's sorption by several orders of magnitude. Based on theoretical results, we offer a speculative model for the detection of non-self lipid bilayers by the RES.

Structure-affinity relationships of arylquinolizines at alpha-adrenoceptors

Hexahydroaryl[a]quinolizines comprise a prominent structural element in several alpha 2-adrenoceptor antagonists. Eight hexahydroheteroarylquinolizines were prepared as minimal ligands to investigate the relationship between the nature of the aromatic ring and affinity of these molecules for alpha-adrenoceptors. Affinity for alpha 1-and alpha 2-adrenoceptors was assessed by displacement of [3H]prasozin and [3H]clonidine, respectively. Lipophilicity of the aryl portion of the molecules, reflected by their partition coefficient between octanol and pH 7.4 buffer, correlated well with affinity at both receptor subtypes. Although some compounds showed nanomolar affinity for alpha-adrenoceptors, no subtype selectivity was observed. These results suggest that the aromatic ring enhances binding at both receptors chiefly through hydrophobic interactions and contributes little to subtype selectivity.

Cholecystokinin innervation of rat thalamus, including fibers to ventroposterolateral nucleus from dorsal column nuclei

The distribution of cholecystokinin octapeptide immunoreactive fibers and puncta in the adult rat thalamus was studied using immunocytochemical methods. Small to moderate numbers of immunoreactive fibers were present in the lateral habenular nucleus, ventral lateral geniculate nucleus, zona incerta, parataenial, mediodorsal, medioventral, and submedial nuclei, the rhomboid, paracentral, central lateral and parafascicular nuclei, and in the medial geniculate and dorsal lateral geniculate nuclei. Moderate to large numbers of cholecystokinin (CCK)-positive fibers were present in the paraventricular nuclei, the reticular nucleus, the anteroventral, anteromedial, and central medial nuclei, and in the rostral extension of the internal medullary lamina between the parataenial and anteroventral nuclei. Dense concentrations of immunoreactive fibers were also found in a principal sensory relay nucleus, the ventroposterolateral nucleus (VPL), of the ventrobasal complex. The number of CCK-positive fibers in VPL showed a marked unilateral decrease in rats which had received lesions of the contralateral gracile and cuneate nuclei. The results of this study demonstrate that CCK-immunoreactive fibers and puncta are widely distributed in the rat thalamus, and that the source of these fibers in VPL is probably the dorsal column nuclei.

A decrease in the number of GABAergic somata is associated with the preferential loss of GABAergic terminals at epileptic foci

Previous studies have indicated that a loss of GABAergic terminals occurs at epileptic foci. The present study was undertaken to investigate if this loss is associated with a loss of GABAergic neuronal somata. Seven juvenile monkeys (M. mulatta) received alumina gel injections to the pre-central gyrus of the left cerebral hemisphere to produce epileptic foci. Four of these monkeys were chosen for further quantitative study. One was sacrificed prior to seizure onset ('pre-seizure'), one had seizures for 3 days ('acute'), and two had a seizure record of one month ('chronic'). Sections of tissue from the epileptic cortex and from the contralateral, non-epileptic cortex were processed for glutamate decarboxylase (GAD) immunocytochemistry at the light microscopic level. Quantitative analysis revealed that a loss of GAD-positive neuronal somata ranging from 24 to 52% occurred at epileptic foci for all monkeys. This decrease was significant (P less than 0.01) for the two chronic monkeys. There was also a slight decrease in GAD-positive neurons 1 cm distal to the focus ('parafocus') in the chronic monkeys, but not in the acute or pre-seizure animals. In addition, small GAD-positive somata (50-150 micron2) were more severely decreased in number at epileptic foci than larger ones (200-250 micron2). As an experimental control, an additional monkey was given a surgical lesion in area 4 of one cerebral hemisphere. It did not display seizure activity prior to sacrifice and did not show a loss of GAD-positive neurons proximal to the control lesions. The results of this study indicate that a loss of GABAergic neuronal somata is associated with a loss of GABAergic terminals at epileptic foci, and that this loss may be more specific for the small GABAergic neurons.

Synthesis and evaluation of a prototypal artificial red cell

A new process allows microencapsulation of purified human hemoglobin and 2,3-diphosphoglycerate to form neohemocytes. The microcapsule membrane is composed of phospholipids and cholesterol. Neohemocytes are substantially smaller than erythrocytes, contain 15.1 grams per decaliter of hemoglobin, and have a P50 value (the partial pressure of oxygen at which the hemoglobin is half-saturated) of 24.0 torr. All rats given 50-percent exchange transfusions survived with only limited evidence of reversible toxicity. Normal serum glutamate-pyruvate-transaminase values at 1, 7, and 30 days after transfusion were consistent with minimal hepatotoxicity. The concentration of blood urea-nitrogen was elevated by 35 percent after 1 day but returned to normal by day 7. However, histopathology revealed normal kidneys on day 1 as well as on days 7 and 30. Neohemocytes cleared from the circulation of transfused rats with an apparent half-life of 5.8 hours.

Transarticular pinning for repair of hip dislocation in the dog: a retrospective study of 40 cases

Transarticular pinning was used for the repair of hip dislocation in 40 dogs. The mean follow-up period was 18.4 months. Satisfactory results were achieved in 80% of the cases. Body weight, ipsilateral femoral head fracture, and hip dysplasia appeared to affect long-term prognosis. The most frequent complication was pin breakage, but this did not affect final outcome and could be avoided by using pins of larger diameter. Osteonecrosis was observed in two cases.

Lymphatic transport of liposome-encapsulated agents: effects of liposome size following intraperitoneal administration

Liposomal encapsulation can limit passage of a drug from a peritoneal administration site to blood, while enhancing lymphatic transport. We evaluated the effects of liposome size on lymphatic transport after intraperitoneal administration. Liposomes tested had mean diameters of either 0.72, 0.46, 0.17, or 0.048 micron and identical compositions. [14C]Sucrose was the aqueous space marker (model drug). Doses were given to thoracic-duct-cannulated rats. The subsequent 0-5 h time-course of carbon-14 was quantified in thoracic lymph, several lymph nodes, blood, and urine. Calibration studies indicated a maximum of approximately 30% of the absorbed dose could be collected in thoracic lymph. Carbon-14 levels in the various nodes covered a 1000-fold range, and relatively high levels were observed in the left mediastinal, parathymic, cisternal, and renal lymph nodes. Liposome stability in vivo and in vitro increased with decreasing size. Absorption from the peritoneal cavity was independent of size. The smallest liposomes were collected in lymph with little lymph node retention. The largest liposomes were retained most by lymph nodes, and would be the best prototypical carrier of the group if increased therapeutic availability within both lymph and lymph nodes is desired. The results implicate other, unexplored physical and physiological variables as potentially of equal importance.

Stimulated emission and tunable gain from Rh(2+) ions in RbCaF(3) crystals

Stimulated emission was detected in RbCaF(3):Rh(2+) crystals through the observation of power-dependent shortening of the fluorescence lifetime and narrowing of the emission band with a distinct threshold. In addition, single-pass gain was observed to be tunable between about 700 and 720 nm.