Molecular dynamics simulations of acyclic analogs of nucleic acids for antisense inhibition.

For antisense applications, oligonucleotides must be chemically modified to be resistant to endogenous nucleases. Until now, antisense oligonucleotide (ASO) analogs have been synthesized and then tested for their ability to duplex with a target nucleic acid, usually RNA. In this work, using molecular dynamics calculations simulations, we systematically tested a series of chemically modified analogs in which the 2-deoxyribose was substituted for by one or two methylene groups on each side of the phosphate backbone, producing four compounds, of which three were previously unknown. We used a 9-mer sequence of which the solution structure has been determined by NMR spectroscopy and tested the ability to form stable duplexes of these acyclic analogs to both DNA and RNA. In only one case out of eight, we unexpectedly found the formation of a stable duplex with complementary RNA. We also applied limitations on end fraying because of the terminal AT base pairs, in order to eliminate this as a factor in the comparative results. We consider this a predictive method to potentially identify target ASO analogs for synthesis and testing for antisense drug development.

31P-magnetic resonance spectra of ovarian cancer cells exposed to chemotherapy within a three-dimensional Matrigel construct.

We aimed to determine the metabolic profile and effects of chemotherapy on ovarian cancer cell metabolism in a three-dimensional (3D) vs. a two-dimensional (2D) construct using 31P-magnetic resonance spectroscopy (MRS). Three ovarian cancer cell lines were embedded in a 3D perfused Matrigel construct or grown in a 2D monolayer. Metabolic differences between the three cell lines were determined using 31P-MRS both in the 3D and in the 2D constructs. Cells were incubated with three different cytotoxic drugs at LC50 for 44 h and evaluated for metabolic changes using 31P-MRS. While the 3D construct allowed MRS assessment of viable cells, the 2D monolayer permitted evaluation of non-viable cell extracts. In both cells embedded in Matrigel (CEM) and cells grown in monolayers (CGM) different cancer cell lines showed characteristic metabolic fingerprints, which differed significantly between CEM and CGM. In contrast to the cell monolayer, CEM allowed continuous monitoring of the changes in 31P-MRS spectra over time following exposure to chemotherapy, demonstrating a progressive decrease in specific phosphorylated metabolites. The metabolic response of CEM and CGM to various antimitotic agents was significantly different. We conclude that different ovarian cancer cell lines show characteristic 31P-MRS fingerprints and specific metabolic changes in response to cytotoxic drug treatment. The perfused 3D Matrigel construct is superior to the 2D tissue monolayer for 31P-MRS studies, because it simulates the in vivo conditions more closely and facilitates MRS evaluation of viable cells as well as continuous monitoring of metabolic changes in response to chemotherapy over time.

Oxidative stress causes membrane phospholipid rearrangement and shedding from RBC membranes--an NMR study.

Nuclear Magnetic Resonance (NMR) spectroscopy was used to investigate the relationship between oxidative stress experienced by RBCs and their phospholipid content and shedding. Using 1H-NMR, we demonstrated a higher lactate/pyruvate ratio, an indicator of oxidative stress, in normal RBCs treated with oxidants (t-butylhydroxyperoxide and H2O2) as well as in beta-thalassemic RBCs. Using 31P-NMR, we found 30% more phosphatidylcholine (PC), and unexpectedly, 35% less phosphatidylserine (PS) in the thalassemic RBCs. PS was decreased by treatment with oxidants and increased by anti-oxidants (vitamin C and N-acetyl cysteine); PC showed the opposite behavior. Thalassemic RBCs incubated in phosphate buffered saline produced more PS in the supernatant than normal RBCs. Anti-oxidants reduced the PS in the supernatant while oxidants increased it. Plasma of thalassemic patients contained 2.6-fold and 1.8-fold more PS and PC, respectively, than normal plasma. These results indicate that the decreased PS in RBCs resulted from increased shedding. The nature of the shed PS was studied by purifying and analyzing membranous microparticles from the plasma and RBC supernatants. More PS was found in microparticles purified from thalassemic plasma and RBC supernatants (5.6- and 4.8-fold, respectively) than in their normal counterparts. However, the bulk (80-90%) of the shed PS was not associated with microparticles. The significance of PS shedding for RBC survival needs further clarification.

Specific lipoplex-mediated antisense against Bcl-2 in breast cancer cells: a comparison between different formulations.

G3139 is an antisense oligonucleotide (ODN) that can down-regulate bcl-2, thus potentially acting as a potent anticancer drug. However, effective therapy requires efficient ODN delivery, which may be achieved by employing G3139 lipoplexes. Yet, lipofection is a complex, multifactorial process that is still poorly understood. In order to shed more light on this issue, we prepared 18 different G3139 lipoplex formulations and compared them in terms of their capability to transfect MCF-7 breast cancer cells. Each formulation was composed of a cationic lipid and sometimes a helper lipid. The cationic lipid was either DOTAP (N-(1-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride), DC-CHOL (3ss[N-(N',N'-dimethylaminoethane)carbamoyl]-cholesterol), or CCS (ceramide carbomoyl spermine). The helper lipid was either DOPC, DOPE, or cholesterol. Each lipid combination existed in two different structural forms--either large unilamellar vesicles (approximately 100 nm LUV) or unsized heterolamellar vesicles (UHV). Cell proliferation assays were used to evaluate the cytotoxicity of G3139 lipoplexes, control cationic lipid assemblies, and free G3139. Western blots were used to confirm the specific activity of G3139 as an anti-bcl-2 antisense agent. We determined that treatment of MCF-7 cells with G3139:CCS lipoplexes (UHV-derived) produced a maximal 50-fold improvement in antisense efficacy compared to treatment with free G3139. The other G3139 lipoplexes were not superior to free G3139. Thus, successful lipofection requires precise optimization of lipoplex lipid composition, structure, and concentration.

Hormone sensitivity is reflected in the phospholipid profiles of breast cancer cell lines.

We have found that the profiles of total phospholipids in malignant breast cancer cell lines change going from hormone sensitive to highly hormone resistant cells lines. In particular, two phospholipid components that were absent or at very low levels in hormone sensitive MCF7 cells and moderately hormone sensitive cell lines (MIII, LCC2) were found in relatively high proportions in highly hormone resistant cell lines (MB435, MB231). These two components were shown to be the alkylacylphosphatidylcholine (AAPtdC) and the unsaturated analog plasmenylphosphatidylethanolamine (plasmenyl-PtdE). Another component phosphatidylethanolamine (PtdE) increased in correlation with the degree of hormone insensitivity. This was shown using 31P NMR spectroscopy of lipid extracts of the cells, and was confirmed using HPLC analysis, as well as other techniques. The significance of these results for the metabolic characteristics of these cell lines is related to the therapeutic responsiveness of breast cancer.

High-b-value diffusion-weighted MR imaging for pretreatment prediction and early monitoring of tumor response to therapy in mice.

PURPOSE: To evaluate the use of diffusion-weighted magnetic resonance (MR) imaging with standard and high b values for pretreatment prediction and early detection of tumor response to various antineoplastic therapies in an animal model. MATERIALS AND METHODS: Mice bearing C26 colon carcinoma tumors were treated with doxorubicin (n = 25) and with aminolevulinic acid-based photodynamic therapy (n = 23). Fourteen mice served as controls. Conventional T2-weighted fast spin-echo and diffusion-weighted MR images were acquired once before therapy and at 6, 24, and 48 hours after treatment. Pretreatment and early (1-2 days) posttreatment water diffusion parameters were calculated and compared with later changes in tumor volumes measured on conventional MR images by using the Pearson correlation test. RESULTS: In chemotherapy-treated tumors, a significant correlation (P <.002, r = 0.6) was observed between diffusion parameters that reflected tumor viability, measured prior to treatment, and changes in tumor volumes after therapy. This correlation implies that tumors with high pretreatment viability will respond better to chemotherapy than more necrotic tumors. In tumors treated with photodynamic therapy, no such correlation was found. Changes observed in water diffusion 1-2 days after treatment significantly correlated with later tumor growth rate for both therapies (P <.002, r = 0.54 for photodynamic therapy; P <.0003, r = 0.61 for chemotherapy). CONCLUSION: High-b-value diffusion-weighted MR imaging has potential use for the early detection of response to therapy and for predicting treatment outcome prior to initiation of chemotherapy.

Determination of intracellular pH and compartmentation using diffusion-weighted NMR spectroscopy with pH-sensitive indicators.

The intracellular pH (pHi) of a series of cancer cell lines was determined using the pH-sensitive indicators imidazole (Im) or histidine (His) and diffusion-weighted (DW) proton NMR spectroscopy. The DW method allows the observation at high magnetic field gradient values of only the slow-moving (intracellular) components, thus ensuring complete separation between intra- and extracellular components. Using the chemical shift difference (deltadelta) between the imidazole ring C2-H and C4(5)-H peaks, we were able to measure the pHi independently of chemical shift standardization. With His, the cell lines gave pHi values of approximately 6.5-7.0, whereas with Im, a second, more acidic compartment (pHi = 5.5-5.8) was also observed. An inverse correlation was also found between pHi and the intracellular lactate concentration. This method may be applicable to in vivo pH determinations.

Early detection of response to radiation therapy in patients with brain malignancies using conventional and high b-value diffusion-weighted magnetic resonance imaging.

PURPOSE: To study the feasibility of using diffusion-weighted magnetic resonance imaging (DWMRI), which is sensitive to the diffusion of water molecules in tissues, for detection of early tumor response to radiation therapy; and to evaluate the additional information obtained from high DWMRI, which is more sensitive to low-mobility water molecules (such as intracellular or bound water), in increasing the sensitivity to response. PATIENTS AND METHODS: Standard MRI and DWMRI were acquired before and at regular intervals after initiating radiation therapy for 10 malignant brain lesions in eight patients. RESULTS: One week posttherapy, three of six responding lesions showed an increase in the conventional DWMRI parameters. Another three responding lesions showed no change. Four nonresponding lesions showed a decrease or no change. The early change in the diffusion parameters was enhanced by using high DWMRI. When high DWMRI was used, all responding lesions showed increase in the diffusion parameter and all nonresponding lesions showed no change or decrease. Response was determined by standard MRI 7 weeks posttherapy. The changes in the diffusion parameters measured 1 week after initiating treatment were correlated with later tumor response or no response (P <.006). This correlation was increased to P <.0006 when high DWMRI was used. CONCLUSION: The significant correlation between changes in diffusion parameters 1 week after initiating treatment and later tumor response or no response suggests the feasibility of using DWMRI for early, noninvasive prediction of tumor response. The ability to predict response may enable early termination of treatment in nonresponding patients, prevent additional toxicity, and allow for early changes in treatment.