Insulin regulates alternative splicing of protein kinase C beta II through a phosphatidylinositol 3-kinase-dependent pathway involving the nuclear serine/arginine-rich splicing factor, SRp40, in skeletal muscle cells.

Insulin regulates the inclusion of the exon encoding protein kinase C (PKC) betaII mRNA. In this report, we show that insulin regulates this exon inclusion (alternative splicing) via the phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway through the phosphorylation state of SRp40, a factor required for insulin-regulated splice site selection for PKCbetaII mRNA. By taking advantage of a well known inhibitor of PI 3-kinase, LY294002, we demonstrated that pretreatment of L6 myotubes with LY294002 blocked insulin-induced PKCbetaII exon inclusion as well as phosphorylation of SRp40. In the absence of LY294002, overexpression of SRp40 in L6 cells mimicked insulin-induced exon inclusion. When antisense oligonucleotides targeted to a putative SRp40-binding sequence in the betaII-betaI intron were transfected into L6 cells, insulin effects on splicing and glucose uptake were blocked. Taken together, these results demonstrate a role for SRp40 in insulin-mediated alternative splicing independent of changes in SRp40 concentration but dependent on serine phosphorylation of SRp40 via a PI 3-kinase signaling pathway. This switch in PKC isozyme expression is important for increases in the glucose transport effect of insulin. Significantly, insulin regulation of PKCbetaII exon inclusion occurred in the absence of cell growth and differentiation demonstrating that insulin-induced alternative splicing of PKCbetaII mRNA in L6 cells occurs in response to a metabolic change.

Fully modified 2' MOE oligonucleotides redirect polyadenylation.

Many genes have been described and characterized that have alternative polyadenylation signals at the 3'-end of their pre-mRNAs. Many of these same messages also contain destabilization motifs responsible for rapid degradation of the mRNA. Polyadenylation site selection can thus determine the stability of an mRNA. Fully modified 2'-O:-methoxy ethyl/phosphorothioate oligonucleotides that hybridize to the 3'-most polyadenylation site or signal of E-selectin were able to inhibit polyadenylation at this site and redirect it to one of two upstream cryptic sites. The shorter transcripts produced after antisense treatment have fewer destabilization sequences, increased mRNA stability and altered protein expression. This study demonstrates that antisense oligonucleotides can be successfully employed to redirect polyadenylation. This is the first demonstration of the use of oligonucleotides to increase, rather than decrease, abundance of a message.

Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity.

Design of antisense oligonucleotides targeting any mRNA can be much more efficient when several activity-enhancing motifs are included and activity-decreasing motifs are avoided. This conclusion was made after statistical analysis of data collected from >1000 experiments with phosphorothioate-modified oligonucleotides. Highly significant positive correlation between the presence of motifs CCAC, TCCC, ACTC, GCCA and CTCT in the oligonucleotide and its antisense efficiency was demonstrated. In addition, negative correlation was revealed for the motifs GGGG, ACTG, AAA and TAA. It was found that the likelihood of activity of an oligonucleotide against a desired mRNA target is sequence motif content dependent.

Patterns of variant polyadenylation signal usage in human genes.

The formation of mature mRNAs in vertebrates involves the cleavage and polyadenylation of the pre-mRNA, 10-30 nt downstream of an AAUAAA or AUUAAA signal sequence. The extensive cDNA data now available shows that these hexamers are not strictly conserved. In order to identify variant polyadenylation signals on a large scale, we compared over 8700 human 3' untranslated sequences to 157,775 polyadenylated expressed sequence tags (ESTs), used as markers of actual mRNA 3' ends. About 5600 EST-supported putative mRNA 3' ends were collected and analyzed for significant hexameric sequences. Known polyadenylation signals were found in only 73% of the 3' fragments. Ten single-base variants of the AAUAAA sequence were identified with a highly significant occurrence rate, potentially representing 14.9% of the actual polyadenylation signals. Of the mRNAs, 28.6% displayed two or more polyadenylation sites. In these mRNAs, the poly(A) sites proximal to the coding sequence tend to use variant signals more often, while the 3'-most site tends to use a canonical signal. The average number of ESTs associated with each signal type suggests that variant signals (including the common AUUAAA) are processed less efficiently than the canonical signal and could therefore be selected for regulatory purposes. However, the position of the site in the untranslated region may also play a role in polyadenylation rate.

Effects of RNA secondary structure on cellular antisense activity.

The secondary and tertiary structures of a mRNA are known to effect hybridization efficiency and potency of antisense oligonucleotides in vitro. Additional factors including oligonucleotide stability and cellular uptake are also thought to contribute to antisense potency in vivo. Each of these factors can be affected by the sequence of the oligonucleotide. Although mRNA structure is presumed to be a critical determinant of antisense activity in cells, to date little direct experimental evidence has addressed the significance of structure. In order to determine the importance of mRNA structure on antisense activity, oligonucleotide target sites were cloned into a luciferase reporter gene along with adjoining sequence to form known structures. This allowed us to study the effect of target secondary structure on oligonucleotide binding in the cellular environment without changing the sequence of the oligonucleotide. Our results show that structure does play a significant role in determining oligonucleotide efficacy in vivo. We also show that potency of oligonucleotides can be improved by altering chemistry to increase affinity for the mRNA target even in a region that is highly structured.

Predicting oligonucleotide affinity to nucleic acid targets.

A computer program, OligoWalk, is reported that predicts the equilibrium affinity of complementary DNA or RNA oligonucleotides to an RNA target. This program considers the predicted stability of the oligonucleotide-target helix and the competition with predicted secondary structure of both the target and the oligonucleotide. Both unimolecular and bimolecular oligonucleotide self structure are considered with a user-defined concentration. The application of OligoWalk is illustrated with three comparisons to experimental results drawn from the literature.

Structure-activity relationships of novel 2-substituted quinazoline antibacterial agents.

High-throughput screening of in-house compound libraries led to the discovery of a novel antibacterial agent, compound 1 (MIC: 12-25 microM against S. pyogenes). In an effort to improve the activity of this active compound, a series of 2-substituted quinazolines was synthesized and evaluated in several antibacterial assays. One such compound (22) displayed improved broad-spectrum antibacterial activity against a variety of bacterial strains. This molecule also inhibited transcription/translation of bacterial RNA, suggesting a mechanism for its antibiotic effects. Structure-activity relationship studies of 22 led to the synthesis of another 24 compounds. Although some of these molecules were found to be active in bacterial growth assays, none were as potent as 22. Compound 22 was tested for its ability to cure a systemic K. pneumonia infection in the mouse and displayed moderate effects compared with a control antibiotic, gentamycin.

A prospective study of the cost-utility of the multichannel cochlear implant.

CONTEXT: Prior clinical studies have indicated that cochlear implantation provides benefits to individuals with advanced sensorineural hearing loss who are unable to gain effective speech recognition with hearing aids. OBJECTIVE: To determine the cost per quality-adjusted life-year (QALY) for adults receiving multichannel cochlear implants. DESIGN: Prospective 12-month multicenter study using preference-based quality-of-life measures and total cost determinations, comparing profoundly hearing-impaired adult subjects with and without cochlear implants. SETTING: Hospital-based and patient-resource clinics. PATIENTS: Severely to profoundly hearing-impaired adult recipients of a cochlear implant and adults eligible for the device who had not yet received it. MAIN OUTCOME MEASURE: Clinical assessment of implant participants included medical and audiologic (speech understanding) data at the time of enrollment, 6 months, and 12 months. All participants' health-utility was assessed at the time of enrollment, 6 months, and 12 months using the Health Utility Index. One-year medical resource utilization and cost data included bills related to implants, patient diaries, charge estimates from clinical sites, and published literature. A decision model was developed to determine cost per QALY. RESULTS: Of the 84 enrolled adults, 62 (75%) completed the study. Mean health-utility scores at the time of enrollment were identical between groups. The marginal 12-month health-utility gain for implant recipients was 0.20; 90% of this improvement was achieved within 6 months. For patients with a mean 22-year life expectancy, the marginal cost per QALY was $14,670. CONCLUSIONS: Overall, multichannel cochlear implants significantly improved recipients' performance on measures of speech understanding and ratings of health-utility within 6 months of implantation. The multichannel cochlear implant yielded a very favorable cost per QALY.

Induction of endogenous Bcl-xS through the control of Bcl-x pre-mRNA splicing by antisense oligonucleotides.

Resistance to apoptosis, which plays an important role in tumors that are refractory to chemotherapy, is regulated by the ratio of antiapoptotic to proapoptotic proteins. By manipulating levels of these proteins, cells can become sensitized to undergo apoptosis in response to chemotherapeutic agents. Alternative splicing of the bcl-x gene gives rise to two proteins with antagonistic functions: Bcl-xL, a well-characterized antiapoptotic protein, and Bcl-xS, a proapoptotic protein. We show here that altering the ratio of Bcl-xL to Bcl-xS in the cell using an antisense oligonucleotide permitted cells to be sensitized to undergo apoptosis in response to ultraviolet B radiation and chemotherapeutic drug treatment. These results demonstrate the ability of a chemically modified oligonucleotide to alter splice site selection in an endogenous gene and illustrate a powerful tool to regulate cell survival.

Trends in educational placement and cost-benefit considerations in children with cochlear implants.

OBJECTIVES: To study the effect of cochlear implantation on the use of educational resources by profoundly hearing-impaired children and to determine trends in educational cost vs benefit. DESIGN: Retrospective study and cost-benefit analysis. SETTING: Outpatient pediatric cochlear implant program in an academic institution (The Listening Center at Johns Hopkins University School of Medicine, Baltimore, Md), in collaboration with public schools in Maryland and surrounding states. PATIENTS OR OTHER PARTICIPANTS: School-aged children with profound prelingual hearing impairment without other clearly defined disabilities. Thirty-five children with multiple-channel cochlear prostheses and a comparison group of 10 children without implants from 'total communication' programs in the Maryland public school system. INTERVENTIONS: Multiple-channel cochlear implantation and at least 1 year of a systematic auditory skill development program at the Listening Center, compared with standard educational management of children with conventional amplification. MAIN OUTCOME MEASURES: Classroom placement and number of hours of special educational support used. RESULTS: A correlation was observed between the length of cochlear implant experience and the rate of full-time placement in mainstream classrooms (r = 0.10; P= .04). There was also a negative correlation between the length of implant experience and the number of hours of special educational support used by fully mainstreamed children (Pearson product moment correlation = -0.10; P = .03). Children with greater than 2 years of implant experience were mainstreamed at twice the rate or more of age-matched children with profound hearing loss who did not have implants. They were also placed less frequently in self-contained classrooms and used fewer hours of special education support. A cost-benefit analysis based on conservative estimates of educational expenses from kindergarten to 12th grade shows a cost savings of cochlear implantation and appropriate auditory (re)habilitation that ranges from $30000 to $200000. CONCLUSIONS: Cochlear implantation accompanied by aural (re)habilitation increases access to acoustic information of spoken language, leading to higher rates of mainstream placement in schools and lower dependence on special education support services. The cost savings that results from a decrease in the use of support services indicates an educational cost benefit of cochlear implant (re)habilitation for many children.

Cost-effectiveness of the diagnostic evaluation of vertigo.

OBJECTIVE: To evaluate the cost-effectiveness of several diagnostic tests used in the evaluation of vertigo. STUDY DESIGN: Cost-effectiveness analysis, using data from retrospective case review. METHODS: Charts and test results were reviewed from 192 outpatients seen in an academic tertiary referral center for evaluation of vertigo. Cost-effectiveness analysis was performed using decision analysis software, data from office and hospital charges, and expert-based estimations of the utility of different test outcomes. Sensitivity analysis was performed using standard algorithms and wide variable ranges. RESULTS: We found that audiologic testing, posturography, and electronystagmography were the most cost-effective tests, and that magnetic resonance imaging and blood tests had the lowest cost-effectiveness. The analysis was sensitive to the effects of financial costs of tests but, with a few exceptions, was typically not sensitive to the utility of test outcomes or the distribution of test results. CONCLUSIONS: The use of cost-effectiveness analysis, the estimation of utility of test outcomes, and techniques of sensitivity analysis should help guide the clinician's decision making on appropriate testing for patients with vertigo.

Inhibition of human immunodeficiency virus type 1 infection in SCID-hu Thy/Liv mice by the G-quartet-forming oligonucleotide, ISIS 5320.

Viral replication was inhibited in a dose-dependent manner after administration of the phosphorothioate oligonucleotide TTGGGGTT (ISIS 5320) to human immunodeficiency virus type 1 (HIV-1)-infected SCID-hu Thy/Liv mice. Potent in vivo antiviral activity was observed against the T-cell-tropic molecular clone NL4-3; the agent was found to have weak activity against one primary HIV-1 isolate, and the agent was inactive against a second primary isolate.

A model of educational resource use by children with cochlear implants.

We have tracked patterns of use of educational and rehabilitative resources as part of an initial assessment of cost-benefit ratios of cochlear implants in children. Forty-two children with cochlear implants in the Listening Center at Johns Hopkins program of aural rehabilitation have served as our study cohort to develop the measures to be assessed. An educational resource matrix stratifies school setting (residential vs special education vs non-specialized "mainstream" setting) and levels of rehabilitative support (speech and language therapy and interpreter use) to map past and current use of these services. Initial cost-benefit projections based on observed advancement toward educational independence in the educational resource matrix indicate an extremely favorable net present value of the implant (cost savings minus cost). These cost-benefit projections will need to be supplemented with measures of the impact on quality of life and future educational and vocational options to determine the overall cost-effectiveness of cochlear implants in children.

Recent trends in utilization of procedures in otolaryngology-head and neck surgery.

The development of minimally invasive techniques and increasing performance of surgery in outpatient settings have had a major influence on otolaryngology-head and neck surgery (OLHNS), but little is known about the extent to which these forces have affected the overall distribution and total rate of performance of OLHNS procedures. The aims of this study were to determine whether there has been a change in the total number of people undergoing OLHNS procedures between 1989 and 1992 in Maryland and to identify those procedures for which there has been a significant change in utilization. Data were obtained on 171,579 patients undergoing OLHNS procedures between 1989 and 1992 in Maryland's nonfederal, acute care hospitals, hospital-based outpatient centers, and freestanding multispecialty surgical centers. Age-adjusted annual surgical rates were calculated by direct standardization using 1990 Maryland census data, and changes in rates over time were examined using linear regression. From 1989 to 1992, there was no significant change in the total age-adjusted annual rate of performance of the most commonly performed OLHNS procedures (P>0.05), yet there was a significant increase (P<0.05) in the rates of ethmoidectomy from 37/100,000 to 73/100,000, intranasal antrotomy from 25/100,000 to 44/100,000, and septoplasty from 70/100,000 to 89/100,000, and a significant decrease (P>0.05) in the rate of rhinoplasty from 44/100,000 to 36/100,000. The data show an annual average decrease in inpatient surgery of 5.2% (P=0.006), and a corresponding increase in outpatient surgery of 5.1% (P=0.005). Maryland surgery rates for commonly performed procedures in OLHNS remained stable overall, except for an increase in sinus surgery and septoplasty rates and a decrease in rhinoplasty rates.

Strategies for rapid deconvolution of combinational libraries: comparative evaluation using a model system.

Synthesis and testing of complex mixtures maximize the number of compounds that can be prepared and tested in a combinatorial library. When mixtures of compounds are screened, however, the identity of the compound(s) selected may depend on the deconvolution procedure employed. Previously, we developed a model system for evaluation of deconvolution procedures and used it to compare pooling strategies for iterative and noniterative deconvolution [Freier et al. J. Med. Chem. 1995, 38, 344-352]. We have now extended the model studies to include simulations of procedures with overlapping subsets such as subtractive pooling [Carell et al. Angew, Chem., Int. Ed. Engl. 1994, 33, 2061-2064], bogus coin pooling [Blake and Litzi-Davis. Bioconjugate Chem. 1992, 3, 510-513], and orthogonal pooling [D'Prez et al. J. Am. Chem. Soc. 1995, 117, 5405-5406]. These strategies required synthesis and testing of fewer subsets than did the more traditional nonoverlapping iterative strategies. The compounds identified using simulations of these strategies, however, were not the most active compounds in the library and were substantially less active than those identified by simulations of more traditional strategies.

Cost utility of the multichannel cochlear implants in 258 profoundly deaf individuals.

Cost utility analysis is a method of cost-effectiveness analysis which provides results in terms of cost per quality-adjusted life-year (QALY). Cost utility for the multichannel cochlear implant was calculated using Ontario Health Utilities Index data from 229 Nucleus 22-channel implant users and 32 cochlear implant candidates awaiting surgery. The health utility of the implanted group was greater than that of the candidate group by 0.204 (P<.0001). Use of this figure in a cost utility calculation indicates that cochlear implantation costs approximately $15,928 per QALY provided. Sensitivity analysis, a technique which systematically varies the assumptions underlying the calculations, suggests a range for the true value of between $12,000 and $30,000. This compares very favorably with other medical interventions. It is concluded that profound hearing loss has a significant effect on quality of life, and measurement of the changes that result from cochlear implant use indicates that this technology provides significant improvements and is quite cost-effective.

Deconvolution of combinatorial libraries for Drug discovery: theoretical comparison of pooling strategies.

Synthesis and testing of mixtures of compounds in a combinatorial library allow much greater throughput than synthesis and testing of individual compounds. When mixtures of compounds are screened, however, the possibility exists that the most active compound will not be identified. The specific strategies employed for pooling and deconvolution will affect the likelihood of success. We have used a nucleic acid hybridization example to develop a theoretical model of library deconvolution for a library of more than 250,000 compounds. This model was used to compare various strategies for pooling and deconvolution. Simulations were performed in the absence and presence of experimental error. We found iterative deconvolution to be most reliable when active molecules were assigned to the same subset in early rounds. Reliability was reduced only slightly when active molecules were assigned randomly to all subsets. Iterative deconvolution with as many as 65,536 compounds per subset did not drastically reduce the reliability compared to one-at-a-time testing. Pooling strategies compared using this theoretical model are compared experimentally in an accompanying paper.

Deconvolution of combinatorial libraries for drug discovery: experimental comparison of pooling strategies.

An experimental evaluation of several different pooling strategies for combinatorial libraries was conducted using a library of 810 compounds and an enzyme inhibition assay (phospholipase A2). The library contained compounds with varying degrees of activity as well as inactive compounds. The compounds were synthesized in groups of three and pooled together in various formats to realize different pooling strategies. With one exception, all iterative deconvolution strategies and position scanning resulted in identification of the same compound. The results are in good agreement with the predicted outcome from theoretical and computational methods. These data support the tenet that active compounds for pharmaceutically relevant targets can be successfully identified from combinatorial libraries organized in mixtures.

Kinetics of G-quartet-mediated tetramer formation.

The phosphorothioate and phosphodiester oligodeoxynucleotides d(TTGGGGTT) form parallel-stranded tetramer structures stabilized by guanosine quartets. The phosphorothioate tetramer has been shown to inhibit human immunodeficiency virus (HIV) in vitro. The kinetics of association and dissociation of both tetramers have been determined as a function of temperature using size exclusion chromatography to measure the ratio of single strand to tetramer. In phosphate buffered saline (pH 7.2) at 37 degrees C, the fourth-order association rate of the phosphorothioate tetramer was 6.1 (+/- 0.5) x 10(4) M-3 s-1; the dissociation rate was 8.2 (+/- 0.2) x 10(-6) min-1, resulting in a t(1/2) of about 60 days. The association rate of the phosphodiester was about one order of magnitude faster and the dissociation rate about one order of magnitude slower than that of the phosphorothioate tetramer. The association reaction had a negative energy of activation for both compounds. Despite thermodynamic instability of the tetramer at low concentrations, the extremely slow dissociation rate may allow use of the phosphorothioate tetramer for AIDS chemotherapy.

'Mutational SURF': a strategy for improving lead compounds identified from combinatorial libraries.

Synthesis and testing of mixtures of compounds in a combinatorial library offers the potential of much greater throughput than the 'one compound, one well' approach. When mixtures of compounds are screened, however, pooling and deconvolution strategies must be employed to identify the most active compound in the library. The possibility exists that the most active compound will not be identified. We have developed a theoretical model of library deconvolution using the well characterized properties of nucleic acid hybridization to calculate activities of individual molecules in libraries of more than 250,000 compounds. Calculations using this model have been employed to evaluate strategies for pooling and deconvolution. In the presence of errors in synthesis and testing, iterative deconvolution or position scanning sometimes identified a compound with sub-optimal activity. We describe a procedure called 'mutational SURF' in which 'mutants' of the selected compound are individually synthesized and tested. Simulations of mutational SURF using our model libraries suggest that mutational SURF provides an efficient method for improving the activity of lead compounds identified from combinatorial libraries.