Oligonucleotide inhibitors of human thrombin that bind distinct epitopes.

Thrombin, a multifunctional serine protease, recognizes multiple macromolecular substrates and plays a key role in both procoagulant and anticoagulant functions. The substrate specificity of thrombin involves two electropositive surfaces, the fibrinogen-recognition and heparin-binding exosites. The SELEX process is a powerful combinatorial methodology for identifying high-affinity oligonucleotide ligands to any desired target. The SELEX process has been used to isolate single-stranded DNA ligands to human thrombin. Here, a 29-nucleotide single-stranded DNA ligand to human thrombin, designated 60-18[29], with a Kd of approximately 0.5 nM is described. DNA 60-18[29] inhibits thrombin-catalyzed fibrin clot formation in vitro. Previously described DNA ligands bind the fibrinogen-recognition exosite, while competition and photocrosslinking experiments indicate that the DNA ligand 60-18[29] binds the heparin-binding exosite. DNA 60-18[29] is a quadruplex/duplex with a 15-nucleotide "core" sequence that has striking similarity to previously described DNA ligands to thrombin, but binds with 20 to 50-fold higher affinity. The 15-nucleotide core sequence has eight highly conserved guanine residues and forms a G-quadruplex structure. A single nucleotide within the G-quadruplex structure can direct the DNA to a distinct epitope. Additional sequence information in the duplex regions of ligand 60-18[29] contribute to greater stability and affinity of binding to thrombin. A low-resolution model for the interaction of DNA 60-18[29] to human thrombin has been proposed.

Isolation and characterization of 2'-fluoro-, 2'-amino-, and 2'-fluoro-/amino-modified RNA ligands to human IFN-gamma that inhibit receptor binding.

CD4+ Th cells produce cytokines that play a pivotal role in the induction and regulation of cell-mediated and humoral immunity. Th1 cells, characterized by their secretion of IFN-gamma, induce macrophage cytotoxicity, delayed hypersensitivity, and enhanced cellular immunity. Secretion of IFN-gamma may even suppress Th2-enhanced humoral immunity. A counterproductive Th1 response and concomitant secretion of IFN-gamma may result in inflammatory and autoimmune diseases. IFN-gamma regulation of T cell function has potential for therapeutic intervention. To isolate high affinity oligonucleotide inhibitors of IFN-gamma activity, combinatorial libraries of RNA molecules modified at the 2' position of pyrimidine nucleotides with fluoro (F), amino (NH2), or a mixture of F and NH2 (2'-F/NH2) were screened using the SELEX (systematic evolution of ligands by exponential enrichment) combinatorial chemistry process. Each modified library of RNA molecules provides an expanded repertoire of molecules with increased structural diversity and unique binding properties. This added diversity increases the possibility of isolating molecules with the desired functional properties. These RNAs modified at the 2' position have also been shown to be nuclease resistant. High affinity ligands to human IFN-gamma from each modified library were isolated and characterized. The K(d)s of these ligands were determined and their secondary structures were predicted. The specificity of these ligands for IFN-gamma binding was confirmed, and their ability to inhibit binding of IFN-gamma to its receptor on A549 human lung carcinoma cells was determined. A 2'-NH2-modified ligand (2'-NH2-30) is described that binds IFN-gamma with high affinity and inhibits IFN-gamma-induced expression of MHC class I and ICAM-1 by human myeloid leukemia cells.

Role of phosphorylation on DNA binding and transcriptional functions of human progesterone receptors.

To study the function of human progesterone receptor (hPR) phosphorylation, we have tested four sets of serine to alanine substitution mutants: 10 serine clusters, located in regions common to both hPR isoforms (the M-series mutants) were mutated in A-receptors and B-receptors; 6 serine clusters located in the B-upstream segment (BUS; the B-series mutants) were mutated individually and collectively and cloned into B-receptors and into BUS-DBD-NLS, a constitutive transactivator, in which the AF3 function of BUS is fused to the DNA binding domain (DBD) and nuclear localization signal (NLS) of hPR. Transcription by most of the M-series mutants resembles that of wild-type A- or B-receptors. Mutation of 3 sites, Ser190 at the N terminus of A-receptors, a cluster of serines just upstream of the DBD, or Ser676 in the hinge region, inhibits transcription by 20-50% depending on cell or promoter context. These sites lie outside the AF1 activation function. M-series mutants are substrates for a hormone-dependent phosphorylation step, and they all bind well to DNA. Progressive mutation of the B-series clusters leads to the gradual dephosphorylation of BUS, but only the 6-site mutant, involving 10 serine residues, is completely dephosphorylated. These data suggest that in BUS alternate serines are phosphorylated or dephosphorylated at any time. However, even when BUS is completely dephosphorylated, both BUS-DBD-NLS and full-length B-receptors remain strong transactivators. Mutant B-receptors also do not acquire the dominant negative properties of A-receptors, and they retain the ability to activate transcription in synergy with 8-Br-cAMP and antiprogestins. We conclude that phosphorylation has subtle effects on the complex transcriptional repertoire that distinguishes the two hPR isoforms and does not influence transactivation mediated by AF1 or AF3, but subserves other functions.

Functional analysis of a mutant estrogen receptor isolated from T47Dco breast cancer cells.

OBJECTIVE: Estrogen receptor-positive cancers that initially respond to hormone therapy often progress to a resistant state. The breast cancer cell line T47Dco is a model for such resistance. It is a polymorphic line, composed of multiple cell populations that demonstrate the presence of mutant estrogen receptors by cloning and sequencing techniques. Our objective was to isolate and analyze the structural and functional characteristics of the T47Dco mutant estrogen receptor complementary deoxyribonucleic acid clones. STUDY DESIGN: We constructed two independent T47Dco complementary deoxyribonucleic acid libraries. We isolated and sequenced T47Dco estrogen receptors and have identified a mutant receptor that is truncated near the end of the deoxyribonucleic acid binding domain. This mutant has now been recreated with site-directed mutagenesis and tested for its ability to bind to deoxyribonucleic acid, dimerize with other estrogen receptors, and activate gene transcription by the chloramphenicol acetyltransferase assay and by gel shift assays. RESULTS: The chloramphenicol acetyltransferase assays reveal that in the absence of estradiol low levels of conversion of chloramphenicol to acetylated products occur when the mutant estrogen receptor is used to activate chloramphenicol acetyltransferase gene transcription, supporting that it has some constitutive function. Also, gel mobility shift assays demonstrate low levels of deoxyribonucleic acid binding with the mutant protein. CONCLUSION: This mutant estrogen receptor may contribute to the estrogen receptor-positive, hormone-resistant phenotype of T47Dco cells by constitutively binding to and activating genes that were previously estradiol dependent.

Hormone-induced progesterone receptor phosphorylation consists of sequential DNA-independent and DNA-dependent stages: analysis with zinc finger mutants and the progesterone antagonist ZK98299.

Human progesterone receptors (hPRs) are phosphorylated at multiple serine residues, first in a basal step and then in a hormone-induced step. To determine whether hormone-induced phosphorylation precedes or follows the interaction of hPRs with DNA two strategies were used. (i) DNA binding was prevented or altered with site-specific mutants of the A form of hPR; (ii) DNA binding of wild-type hPR forms A and B was prevented with the progesterone antagonist ZK98299. Two hPRA mutants were constructed: DBDCys, which lacks a critical cysteine residue in the first zinc finger, and DBDsp, which is mutated at three discriminatory amino acids to change its DNA binding specificity from a progesterone response element to an estrogen response element. Receptors were transiently expressed in PR-negative cells and were intranuclear. DBDCys did not bind DNA in vitro and DBDsp bound only the estrogen response element. Transiently expressed hPRA and DBDsp showed the upward shift in electrophoretic mobility characteristic of hormone-induced phosphorylation; it was absent with DBDCys. Hormone-induced [32P] orthophosphate incorporation into transiently expressed DBDCys was reduced 60% compared to hPRA and DBDsp but was not eliminated. ZK98299 binds hPRs but prevents their interaction with DNA. Compared to R5020, the antagonist reduced phosphorylation of hPRB and hPRA in T47D breast cancer cells by 60% and totally prevented the mobility shift. We conclude that the hormone-induced phosphorylation of hPR includes DNA-independent and DNA-dependent stages and that only DNA-dependent sites contribute to the mobility shift.

Epitope mapping of the anti-human progesterone receptor monoclonal antibody, AB-52.

The monoclonal antibody AB-52 has high affinity and specificity for the two natural human progesterone receptor forms, receptor A (hPRA) and receptor B (hPRB), but it does not bind the PR of chick, mice, rats or rabbits. We have used a novel method to map its epitope. Based on a series of site-directed mutants of hPRA, together with immunoblotting, DNA gel mobility shift and antibody super shift assays, we have mapped the epitope of AB-52 to a 17 amino acid sequence lying between Val221 and Leu237 of the 933 amino acid hPRB protein. This N-terminal sequence is common to both hPRB and hPRA but is missing in chick PR and differs extensively from mouse PR. No anti-rabbit PR antibodies map to the homologous rabbit PR sequence which differs from hPR by four amino acids, suggesting that one or more of these four amino acids form a critical subset of residues in hPR that define the human specificity of AB-52. Knowledge of the AB-52 epitope is useful in structural analysis of PR, and in competition studies. Additionally, this 17 amino acid peptide whose antigenicity would not be predicted from computer analysis, should be useful for generating additional hPR specific antibodies.

Chronic alcoholic cardiomyopathy. Protection of the isolated ischaemic working heart by ribose.

The effects of ribose on the pre- and post-ischaemic functional performance of the isolated working heart from 24 month old chronically alcoholic animals was investigated. The improved perfusion model permitted the isolated heart to perform work analogous to that of the normal physiological load, in a system where systemic pressure and atrial pressure could be altered over a wide range and oxygen loss from the perfusion fluid was a minimum. There was a remarkable improvement in the performance of isolated hearts taken from alcoholic animals that were perfused with 1.7 mM ribose both before and after a 25.0 min period of global myocardial ischaemia (at 25 degrees C), however ribose treatment did not greatly affect the performance of hearts of isocaloric control aged rats. Chronic alcohol consumption significantly affected heart performance, causing a marked reduction in both cardiac and work output. After ischaemia the work of all hearts was notably decreased; there was no work output in untreated hearts of alcoholic animals, whereas in hearts of alcoholic animals treated with ribose work output was only decreased by 35%. The acute response to ribose by hearts of aged chronically alcoholic animals suggests a role for this compound as a positive inotropic agent and clearly indicates the beneficial potential of ribose for inclusion in cardioplegic solutions or for infusion in alcoholic subjects showing signs of heart failure or chronic heart disease.

Isolation and analysis of DNA markers specific to human chromosome 15.

Chromosome-specific DNA markers provide a powerful approach for studying complex problems in human genetics and offer an opportunity to begin understanding the human genome at the molecular level. The approach described here for isolating and characterizing DNA markers specific to human chromosome 15 involved construction of a partial chromosome-15 phage library from a human/Chinese hamster cell hybrid with a single human chromosome 15. Restriction fragments that identified unique- and low-copy loci on chromosome 15 were isolated from the phage inserts. These fragments were regionally mapped to the chromosome by three methods, including Southern analysis with a mapping panel of cell hybrids, in situ hybridization to metaphase chromosomes, and quantitative hybridization or dosage analysis. A total of 42 restriction fragments of unique- and low-copy sequences were identified in 14 phage. The majority of the fragments that have been characterized so far exhibited the hybridization pattern of a unique locus on chromosome 15. Regional mapping assigned these markers to specific locations on chromosome 15, including q24-25, q21-23, q13-14, q11-12, and q11. RFLP analysis revealed that several markers displayed polymorphisms at frequencies useful for genetic linkage analysis. The markers mapped to the proximal long arm of chromosome 15 are particularly valuable for the molecular analysis of Prader-Willi syndrome, which maps to this region. Polymorphic markers in this region may also be useful for definitively establishing linkage with one form of dyslexia. DNA probes in this chromosomal region should facilitate molecular structural analysis for elucidation of the nature of instability in this region, which is frequently associated with chromosomal aberrations.

Immunological studies of propionyl CoA carboxylase in livers and fibroblasts of patients with propionic acidemia.

Antiserum prepared against homogeneous pig heart propionyl CoA carboxylase cross-reacted with human propionyl CoA carboxylase, and was used to demonstrate the presence of immunological cross-reacting material in extracts from the livers of three patients and from fibroblasts of four patients with propionic acidemia representing three major propionyl CoA carboxylase-deficient genetic complementation groups, pcc A, pcc C and bio. Since the quantity of cross-reacting material in the propionyl CoA carboxylase-deficient livers and enzyme-deficient fibroblast cell lines was comparable to that in normal tissues while showing less than five percent of the normal enzyme activity, these patients must synthesize normal or near-normal quantities of an enzymatically inactive propionyl CoA carboxylase protein. In addition, no appreciable change in the amount of cross-reacting material was found in the biotin-responsive bio fibroblasts after incubation with supplemental biotin despite a sixteen-fold increase in enzyme activity suggesting that the defect in the bio mutant involves the activation rather than the synthesis of a pre-existing normal apoenzyme.