Inhibition of c-Jun N-terminal kinase 1, but not c-Jun N-terminal kinase 2, suppresses apoptosis induced by ischemia/reoxygenation in rat cardiac myocytes.

In the present study, rat cardiac myocytes were used as an in vitro ischemia/reperfusion injury model to delineate the role of c-Jun N-terminal kinase (JNK) 1 and JNK2 isoforms in ischemia/reoxygenation-induced apoptosis using an antisense approach. Exposure of rat cardiac myocytes to ischemia did not induce apoptosis as detected by staining with either acridine orange/ethidium bromide or annexin-V-fluorescein/propidium iodide. In contrast, a time-dependent increase in the number of apoptotic cells was noted after reoxygenation of ischemic myocytes, whereas the level of necrotic cells remained unaltered. Reoxygenation, but not ischemia alone, also caused a time-dependent increase in JNK activation that preceded apoptosis induction. Treatment of cardiac myocytes with antisense (AS) oligonucleotides that specifically targeted either JNK1 or JNK2 significantly reduced both mRNA and protein expression of the target isoform but had no effect on the expression of the alternate isoform. Pretreatment of cardiac myocytes with JNK1 AS, but not JNK2 AS, resulted in almost complete attenuation of reoxygenation-induced apoptosis. Furthermore, control oligonucleotides for JNK1 AS or JNK2 AS had no effect on JNK mRNA or protein expression or reoxygenation-induced apoptosis, indicating a sequence-specific mode of action. Additional studies revealed that apoptosis induced by other JNK-activating stimuli, including ceramide, heat shock, and UV irradiation, was partly suppressed after treatment with JNK1 AS but not JNK2 AS. These findings demonstrate that the JNK1 isoform plays a preferential role in apoptosis induced by ischemia/reoxygenation as well as diverse JNK-activating cellular stresses.

Discovery and analysis of antisense oligonucleotide activity in cell culture.

In the past decade antisense oligonucleotides (ASOs) have proven to be a useful tool for dissection of gene function in molecular cell biology (Koller, E., Gaarde, W. A., and Monia, B. P. (2000) Trends Pharm. Sci., 21, 142-148), and validation of gene targets in animal models (Crooke, S. T. (1998) Biotechnol. Gen. Eng. Rev. 15, 121-157), as well as a means for therapeutic treatment of human diseases (Bennett, C. F. (1999) Exp. Opin. Invest. Drugs 8, 237-253). An important step toward usage of ASOs in the described applications is identification of an active ASO. This article describes the underlying basis and means for achieving this goal in cell culture.

In vitro and in vivo inhibition of interleukin (IL)-5-mediated eosinopoiesis by murine IL-5Ralpha antisense oligonucleotide.

The unique role of interleukin (IL)-5 in eosinophil production, activation, and localization makes this cytokine a prime target for therapeutic intervention in diseases characterized by a selective blood and tissue eosinophilia. In an attempt to block the effects of IL-5 on eosinophils, a strategy was developed to suppress the expression of the IL-5 receptor alpha chain (IL-5Ralpha) by antisense oligonucleotides (ASOs). IL-5Ralpha ASOs were identified which selectively and specifically suppress the expression of messenger RNA and proteins of both the membrane and the soluble form of the receptor in constitutively IL-5R-expressing murine BCL-1 cells in vitro. Moreover, these IL-5Ralpha-specific ASOs were able to selectively inhibit the IL-5-induced eosinopoesis from murine fetal liver and bone marrow cells in vitro, suggesting that these molecules may affect the development of IL-5-mediated eosinophilia in vivo. Indeed, intravenous administration of IL-5Ralpha-specific ASOs not only suppressed the bone-marrow and blood eosinophilia in mice after short-term treatment with recombinant murine IL-5 but also inhibited the development of blood and tissue eosinophilia in a ragweed-induced allergic peritonitis model. Thus, blocking the expression of IL-5Ralpha on eosinophil using ASOs may have therapeutic benefits in eosinophilic diseases such as asthma.

Antisense inhibition of membrane-bound human interleukin-5 receptor-alpha chain does not affect soluble receptor expression and induces apoptosis in TF-1 cells.

Binding of human interleukin-5 (HuIL-5) to its membrane-anchored receptor (IL-5R) triggers multiple signaling pathways, cellular proliferation, and maturational responses, as well as protection from apoptosis. In contrast, soluble forms of the HuIL-5R have been shown to inhibit IL-5 signaling and, therefore, may represent naturally occurring negative regulators of IL-5 function. Because of the central role of IL-5 in promoting eosinophilia and airway hyperresponsiveness in animal models of asthma, antisense oligonucleotides specific either for the membrane form alone or for sequences shared between both the membrane and soluble forms of the HuIL-5Ralpha ligand binding chain were designed. The activities of these oligonucleotides were characterized in IL-5R-expressing erythroleukemic TF-1 cells. Herein we report that an antisense oligonucleotide targeted to a sequence unique to the alternatively spliced membrane-bound form of the HuIL-5Ralpha chain has been developed that selectively inhibits membrane, but not soluble, mRNA isoform expression. Both this membrane-specific oligonucleotide and an antisense oligonucleotide targeted to sequence common to both membrane and soluble isoforms were found to potently suppress cell surface IL-5Ralpha levels and IL-5-mediated cell survival by inducing apoptosis similar to IL-5 withdrawal. Thus, these oligonucleotides represent unique genetic agents with therapeutic potential for diseases with an eosinophilic component.

Deletion of individual exons and induction of soluble murine interleukin-5 receptor-alpha chain expression through antisense oligonucleotide-mediated redirection of pre-mRNA splicing.

Expression of the interleukin-5 receptor-alpha (IL-5Ralpha) chain is thought to play an important role in the pathogenesis of asthma and other eosinophilic diseases. With antisense oligonucleotides (ASOs) chemically modified to provide increased hybridization affinity for RNA but that do not support RNase H-mediated cleavage (2'-O-methoxyethyl-modified ASOs), we show that constitutive splicing of murine IL-5Ralpha mRNA can be modulated in cells such that individual exons may be selectively deleted from mature transcripts. Specific deletion of individual exons and redirection of alternative splicing of the IL-5Ralpha mRNA have been achieved with this approach, by targeting 3'-splice sites or exon sequences immediately downstream of an alternative splice site. ASO targeting with these strategies resulted in inhibition of mRNA and protein levels of the membrane IL-5Ralpha isoform capable of signaling IL-5-mediated growth and antiapoptotic signals to eosinophils. Membrane isoform IL-5Ralpha inhibition was coupled with an increase in expression of mRNA for the alternatively spliced soluble isoform, which binds IL-5 extracellularly and may block its function. These observations suggest the potential general therapeutic use of an antisense approach to increase expression of variant RNA transcripts and to thereby produce proteins devoid of specific functional domains that may impact disease processes, as well as its specific utility for modulating expression of a key cytokine receptor implicated in allergic inflammation.

STAT3 regulates the growth and immunoglobulin production of BCL(1) B cell lymphoma through control of cell cycle progression.

STAT3 is constitutively phosphorylated on tyrosine(705) in self-renewing, CD5(+) murine B-1 lymphocytes. Nuclear extracts from untreated primary B-1 or CD5(+) BCL(1) B lymphoma cells were found to contain immunoreactive STAT3 protein that binds to a sis-inducible element present in the promoter of the p21(waf1/cip1) tumor suppressor gene and is constitutively phosphorylated on serine(727). To determine the functional significance of constitutive STAT3 activation in B lymphoma cells, a specific STAT3 antisense oligonucleotide was developed and used to examine basal BCL(1) cell growth and IgM production. Abrogating STAT3 expression in BCL(1) cells inhibited their proliferative capacity and induced a corresponding decrease in secretion of IgM. Cell cycle analysis showed a block in progression through G1 in BCL(1) cells treated with the STAT3 antisense oligonucleotide. These results indicate that STAT3 controls cell growth and immunoglobulin secretion by enhancing progression through the G1 phase of the cell cycle in BCL(1) B cell lymphoma.

Inhibition of antigen-induced eosinophilia and late phase airway hyperresponsiveness by an IL-5 antisense oligonucleotide in mouse models of asthma.

Chronic airway eosinophilia is associated with allergic asthma and is mediated in part by secretion of IL-5 from allergen-specific Th2 lymphocytes. IL-5 is a known maturation and antiapoptotic factor for eosinophils and stimulates release of nascent eosinophils from bone marrow into the peripheral circulation. An antisense oligonucleotide found to specifically inhibit IL-5 expression in vitro was observed to significantly reduce experimentally induced eosinophilia in vivo, in both the murine OVA lung challenge and allergic peritonitis models. Intravenous administration resulted in sequence-dependent inhibition of eosinophilia coincident with reduction of IL-5 protein levels, supporting an antisense mechanism of action. Potent suppression of lung eosinophilia was observed up to 17 days after cessation of oligonucleotide dosing, indicating achievement of prolonged protection with this strategy. Furthermore, sequence-specific, antisense oligonucleotide-mediated inhibition of Ag-mediated late phase airway hyperresponsiveness was also observed. These data underscore the potential utility of an antisense approach targeting IL-5 for the treatment of asthma and eosinophilic diseases.

Characterization of a potent and specific class of antisense oligonucleotide inhibitor of human protein kinase C-alpha expression.

The use of antisense oligonucleotides to inhibit the expression of targeted mRNA sequences is becoming increasingly commonplace. Although effective, the most widely used oligonucleotide modification (phosphorothioate) has some limitations. In previous studies we have described a 20-mer phosphorothioate oligodeoxynucleotide inhibitor of human protein kinase C-alpha expression. In an effort to identify improved antisense inhibitors of protein kinase C expression, a series of 2' modifications have been incorporated into the protein kinase C-alpha targeting oligonucleotide, and the effects on oligonucleotide biophysical characteristics and pharmacology evaluated. The incorporation of 2'-O-(2-methoxy)ethyl chemistry resulted in a number of significant improvements in oligonucleotide characteristics. These include an increase in hybridization affinity toward a complementary RNA (1.5 degrees C per modification) and an increase in resistance toward both 3'-exonuclease and intracellular nucleases. These improvements result in a substantial increase in oligonucleotide potency (>20-fold after 72 h). The most active compound identified was used to examine the role played by protein kinase C-alpha in mediating the phorbol ester-induced changes in c-fos, c-jun, and junB expression in A549 lung epithelial cells. Depletion of protein kinase C-alpha protein expression by this oligonucleotide lead to a reduction in c-jun expression but not c-fos or junB. These results demonstrate that 2'-O-(2-methoxy)ethyl-modified antisense oligonucleotides are 1) effective inhibitors of protein kinase C-alpha expression, and 2) represent a class of antisense oligonucleotide which are much more effective inhibitors of gene expression than the widely used phosphorothioate antisense oligodeoxynucleotides.

Intersubunit communication in tryptophan synthase by carbon-13 and fluorine-19 REDOR NMR.

The beta subunits of the 143-kDa alpha2beta2 tetrameric enzyme tryptophan synthase have been labeled by L-[ring-4-19F]phenylalanine and L-[phenol-4-13C]tyrosine in an effort to monitor the positions of these residues on ligand binding. Of the 13 phenylalanine and 11 tyrosine residues in the beta subunit, only three pairs have labels with 13C-19F separations of less than 6 angstrom. The beta subunit residues Tyr279 and Phe280 (each members of one of the three Tyr-Phe proximate pairs) have been suggested as possible conformational gates on ligand binding. The 188-MHz 19F NMR spectrum of the microcrystalline, double-labeled enzyme complex has five resolved lines under 5-kHz magic-angle spinning and 80-kHz proton dipolar decoupling. The distribution of beta-subunit 19F isotropic shifts is altered by addition of L-[3-13C]-serine to the mother liquor in contact with the microcrystals, consistent with a conformational rearrangement. The 13C label from serine is detected at 28 ppm as a methyl tautomer of bound aminoacrylate. The change in aromatic 19F chemical shifts on binding of serine indicates an alteration in local electric field gradients within the beta subunit. However, rotational-echo double-resonance 13C NMR (with 19F dephasing) shows that the average 13C-19F distance for the three phenylalanine-tyrosine proximate pairs in the beta subunit is changed by less than 1 angstrom.

Enhanced activity of an antisense oligonucleotide targeting murine protein kinase C-alpha by the incorporation of 2'-O-propyl modifications.

We have previously described the characterization of a 20mer phosphorothioate oligodeoxynucleotide (ISIS 4189) which inhibits murine protein kinase C-alpha (PKC-alpha) gene expression, both in vitro and in vivo. In an effort to increase the antisense activity of this oligonucleotide, 2'-O-propyl modifications have been incorporated into the 5'- and 3'-ends of the oligonucleotide, with the eight central bases left as phosphorothioate oligodeoxynucleotides. Hybridization analysis demonstrated that these modifications increased affinity by approximately 8 and 6 degrees C per oligonucleotide for the phosphodiester (ISIS 7815) and phosphorothioate (ISIS 7817) respectively when hybridized to an RNA complement. In addition, 2'-O-propyl incorporation greatly enhanced the nuclease resistance of the oligonucleotides to snake venom phosphodiesterase or intracellular nucleases in vivo. The increase in affinity and nuclease stability of ISIS 7817 resulted in a 5-fold increase in the ability of the oligonucleotide to inhibit PKC-alpha gene expression in murine C127 cells, as compared with the parent phosphorothioate oligodeoxynucleotide. Thus an RNase H-dependent phosphorothioate oligodeoxynucleotide can be modified as a 2'-O-propyl 'chimeric' oligonucleotide to provide a significant increase in antisense activity in cell culture.

Activator carbamino carbon to inhibitor phosphorus internuclear distances in ribulose-1,5-bisphosphate carboxylase/oxygenase. A solid-state NMR study.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a hexadecamer of approximately 550 kDa in most organisms. Rotational-echo double-resonance (REDOR) and transfer-echo double-resonance (TEDOR) solid-state NMR were used to obtain the average internuclear distance between the 99% 13CO2-labeled activator carbamino carbon to the phosphate phosphorus nuclei of active-site-bound 2-carboxy-D-arabinitol 1,5-bisphosphate (CABP), in freeze-quenched, lyophilized samples of confrey Rubisco. The distance 7.5 +/- 0.5 A determined by solid-state NMR is in agreement with the distance of 7.7 A inferred from the crystal-structure coordinates for spinach Rubisco-CABP-CO2-Mg2+ quaternary complex.

Solid-state NMR determination of glyphosate metabolism in a Pseudomonas sp.

The metabolism of the broad-spectrum herbicide, glyphosate (N-phosphonomethylglycine) in a soil Pseudomonas sp. PG2982 has been determined by cross-polarization magic-angle spinning 15N and 13C NMR of intact lyophilized cells. Using samples grown on 13C- and 15N-labeled glyphosate, we find that PG2982 does not metabolize glyphosate to aminomethylphosphonate as has been reported for mixed cultures of soil microbes. Rather, the phosphonomethyl carbon-nitrogen bond in glyphosate is cleaved, releasing glycine. Solid-state NMR analysis reveals that 20% of this glycine is used in the synthesis of purines, 35% is incorporated into protein as glycyl residues, with an additional 35% incorporated as seryl residues. The phosphonomethyl carbon of glyphosate is ultimately incorporated into a number of sites, including the C-2 and C-8 positions of the purine rings of nucleic acids, methyl groups of methionine and thymidine, and the methylene group of serine. The pattern of phosphonomethyl carbon incorporation indicates the involvement of tetrahydrofolate, a coenzyme which facilitates single-carbon transfers. This is the first complete determination of the metabolism of glyphosate in a pure culture, and the first bacterial metabolic study using both single and double cross-polarization solid-state NMR.

Lipid bilayer dynamics and rhodopsin-lipid interactions: new approach using high-resolution solid-state 13C NMR.

High-resolution, solid-state 13C NMR spectra have been obtained for unsonicated multilamellar dispersions of 1,2-dilauryl-sn-glycero-3-phosphocholine (DLPC), recombinant membranes containing DLPC and rhodopsin, and native retinal rod disk membranes. The roles of 1H dipolar decoupling, 1H-13C cross-polarization, and magic-angle sample spinning have been investigated. Rotating-frame 13C relaxation times have been measured and are discussed in terms of lipid bilayer dynamics and rhodopsin-lipid interactions.

[N]NMR determination of asparagine and glutamine nitrogen utilization for synthesis of storage protein in developing cotyledons of soybean in culture.

Solid-state [(15)N]NMR was used to measure the use of the amide and amino nitrogens of glutamine and asparagine for synthesis of storage protein in cotyledons of soybean (Glycine max L. cv. Elf) in culture. No major discrimination in the incorporation of the amide or amino nitrogens of glutamine into protein is apparent, but the same nitrogens of asparagine are used with a degree of specificity. During the first seven days in culture with asparagine as the sole nitrogen source, the amino nitrogen donates approximately twice as much nitrogen to protein as does the amide nitrogen. The use of the amide nitrogen increases with longer periods of culture. The reduced use of the amide nitrogen was confirmed by its early appearance as ammonium in the culture medium. The amide nitrogen of asparagine was found at all times to be an essential precursor for protein because of its appearance in protein in residues whose nitrogens were not supplied by the amino nitrogen. In addition, methionine sulfoximine inhibited growth completely on asparagine, indicating that some ammonium assimilation is essential for storage protein synthesis. These results indicate that in a developing cotyledon, a transaminase reaction is of major importance in the utilization of asparagine for synthesis of storage protein and that, at least in the early stages of cotyledon development, reduced activities of ammonium-assimilating enzymes in the cotyledon tissue or in other tissues of the seed or pod may be a limiting factor in the use of asparagine-amide nitrogen.

N- and [C]NMR determination of utilization of glycine for synthesis of storage protein in the presence of glutamine in developing cotyledons of soybean.

Solid-state (15)N- and [(13)C] NMR have been used to measure quantitatively the utilization of glycine in the presence of glutamine for the synthesis of storage protein in immature cotyledons of soybean (Glycine max L. cv. Elf) in culture. The presence of an equal molar amount of glycine in the medium causes a decrease in the use of glutamine-amide nitrogen. Glycine nitrogen is incorporated extensively into peptide bonds (in amounts greater than what would be expected if it appeared solely in glycine residues), but is used sparingly for synthesis of histidine ring residues, guanidino nitrogen residues of arginine, and lysine residues. The modest use of glycine carbon in protein synthesis does not parallel the use of glycine nitrogen.

Estimation of protein turnover in soybean leaves using magic angle double cross-polarization nitrogen 15 nuclear magnetic resonance.

Magic angle cross-polarization 15N nuclear magnetic resonance spectra of intact lyophilized soybean leaves have been obtained at 9.12 MHz. The leaves were harvested over a 6-week period from 15N-uniformly labeled plants exposed to 13CO2 for 1 to 7 days. The concentration of 13C-15N double labels in the main chains of leaf protein was determined nondestructively by double cross-polarization techniques. Both incorporation and turnover rates of these double labels were estimated and together lead to the conclusion that the protein of a mature, fully expanded soybean leaf is fairly long lived, with a half-life of about 30 days.

Asparagine amide metabolism in developing cotyledons of soybean.

Magic-angle single and double cross-polarization (13)C and (15)N NMR spectra have been obtained of lyophilized soybean cotyledons cultured on media containing, as the only nitrogen source, [4-(13)C, amide-(15)N]asparagine. Single cross-polarization NMR shows directly and unambiguously that both labels from asparagine are incorporated extensively and nonrandomly into protein by the developing cotyledon during a 2-week period. A stable-isotope double label tags a chemical bond. The metabolic fate of the asparagine double label was followed by double cross-polarization NMR using the latter's sensitivity to the dipolar coupling between directly bonded (13)C and (15)N. These experiments show that in culture the direct incorporation of asparagine (with no scrambling of label) accounts for about half of all asparagine residues in soybean protein. This conclusion implies the operation of a regulatory apparatus in soybeans for both direct utilization and degradation of asparagine in protein synthesis.