Carotid and aortic plaque imaging using 3D gradient-echo imaging and the three-point Dixon method with improved motion-sensitized driven-equilibrium (iMSDE).

BACKGROUND: We devised a method that combines the 3D-Dixon-gradientecho (GRE) method with an improved motion-sensitized driven-equilibrium (iMSDE) to suppress blood flow signals. PURPOSE: The purpose of this study was to evaluate the effectiveness of the new method we developed plaque imaging method (3D-Dixon-GRE with the iMSDE method). STUDY TYPE: Retrospective cohort. POPULATION: Thirty-nine patients who underwent cervical plaque imaging. FIELD STRENGTH/SEQUENCE: 3.0 T/3D-GRE. ASSESSMENT: Signal intensities of the common carotid artery, aorta, plaque, muscle, and subcutaneous fat were measured through the VISTA and the 3D-Dixon-GRE with iMSDE methods, and each contrast was calculated. STATISTICAL TEST: Used the Mann Whitney U test. P-values below 0.05 were considered statistically significant. RESULTS: Plaque and muscle contrast estimated through the VISTA method and 3D-Dixon-GRE with iMSDE method was 1.60 ± 0.96 and 2.04 ± 1.06, respectively, (P < 0.05). The contrast between the flow (common carotid artery and Aorta) and muscle according to the VISTA method and 3D-Dixon-GRE with iMSDE method was 0.24 ± 0.11 and 0.40 ± 0.12, respectively (P < 0.001). Finally, the mean contrast for subcutaneous fat and muscle at six locations was 3.05 ± 1.25 and 0.81 ± 0.23 for the VISTA method and 3D-Dixon-GRE with the iMSDE method, respectively (P < 0.001). DATA CONCLUSION: Compared to the conventional method (VISTA), the 3D-Dixon-GRE with iMSDE method is preferable in relation to the fat suppression effect, but it is disadvantageous regarding blood flow signal suppression. Therefore, the 3D-Dixon-GRE with the iMSDE method could be considered useful for plaque imaging.

Relationship between imaging parameters and distortion in magnetic resonance images for gamma knife treatment planning.

In magnetic resonance imaging (MRI), it is necessary to reduce image distortion as much as possible because it suppresses the increase in the planning target volume. This study investigated the relationship between imaging parameters and image distortion when using G-frames. The images were obtained using a 1.5-T MRI system with a 09-101 Pro-MRI phantom. Image distortion was measured by changing the RF pulse mode, gradient mode, asymmetric echo, and bandwidth (BW). The image distortion was increased in the high RF mode than in the Normal mode. The image distortion increased in the following order: Whisper â‰¦ Normal < Fast in the different gradient modes. The image distortion increased in the following order: Without â‰¦ Weak < Strong in the different asymmetric echo modes. The image distortion increased in the following order: 300 Hz/pixel > 670 Hz/pixel â‰§ REF (150 Hz/pixel) in the different Bw. The relationship between parameters and image distortion was clarified in this study when G-frames were used for gamma knife therapy. There is had relationship between the parameters causing variation in the gradient magnetic field and image distortion. Therefore, these parameters should be adjusted to minimize distortion.

Influence of half Fourier and elliptical scanning (radial scan) on magnetic resonance images.

This study aimed to investigate the effect of using slice partial Fourier (SPF), phase partial Fourier (PPF), and radial scan (Elliptical scanning) methods on image quality. Changes in signal-to-noise ratio (SNR), effective slice thickness, and in-plane resolution were measured in 3D-gradient echo when SPF, PPF, and radial scan were used. Effective slice thickness increased and SNR increased when SPF was used; in-plane resolution decreased and SNR decreased when PPF was used; effective slice thickness did not change, in-plane resolution decreased, and SNR increased when the radial scan method was used. The radial scan method reduces image quality and imaging time compared to those in the SPF and PPF methods.

Robust treatment planning in scanned carbon-ion radiotherapy for pancreatic cancer: Clinical verification using in-room computed tomography images.

Purpose: Carbon-ion beam (C-beam) has a sharp dose distribution called the Bragg peak. Carbon-ion radiation therapy, such as stereotactic body radiotherapy in photon radiotherapy, can be completed in a short period by concentrating the radiation dose on the tumor while minimizing the dose to organs at-risk. However, the stopping position of C-beam is sensitive to density variations along the beam path and such variations can lower the tumor dose as well as cause the delivery of an unexpectedly high dose to the organs at risk. We evaluated the clinical efficacy of a robust planning technique considering gastrointestinal gas (G-gas) to deliver accurate radiation doses in carbon-ion radiotherapy for pancreatic cancer. Materials and methods: We focused on the computed tomography (CT) value replacement method. Replacement signifies the overwriting of CT values in the CT images. The most effective replacement method for robust treatment planning was determined by verifying the effects of the three replacement patterns. We selected 10 consecutive patients. Pattern 1 replaces the CT value of the G-gas contours with the value of the region without G-gas (P1). This condition indicates a no-gas state. Pattern 2 replaces each gastrointestinal contour using the mean CT value of each contour (P2). The effect of G-gas was included in the replacement value. Pattern 3 indicates no replacement (P3). We analyzed variations in the target coverage (TC) and homogeneity index (HI) from the initial plan using in-room CT images. We then performed correlation analysis on the variations in G-gas, TC, and HI to evaluate the robustness against G-gas. Results: Analysis of variations in TC and HI revealed a significant difference between P1 and P3 and between P2 and P3. Although no statistically significant difference was observed between P1 and P2, variations, including the median, tended to be fewer in P2. The correlation analyses for G-gas, TC, and HI showed that P2 was less likely to be affected by G-gas. Conclusion: For a treatment plan that is robust to G-gas, P2 mean replacement method should be used. This method does not necessitate any particular software or equipment, and is convenient to implement in clinical practice.

Carbon-Ion Radiotherapy Using Metal Artifact Reduction Computed Tomography in a Patient with Prostate Cancer with Bilateral Hip Prostheses: A Case Report.

Carbon-ion radiotherapy (CIRT) for prostate cancer is both safe and efficacious; beam range calculations use relative stopping power ratio, which is derived from computed tomography (CT) values. However, hip prostheses are made of high atomic number materials and show severe artifacts on CT images. Therefore, it is not possible to accurately calculate dose distribution for CIRT in patients with prostate cancer with hip prostheses. Here, we describe the management of a 77-year-old man with prostate cancer who had previously undergone bilateral hip replacement. CIRT, in combination with androgen deprivation therapy, was recommended as definitive treatment for prostate cancer. Planning CT, magnetic resonance (MRI), and CT images with metal artifact reduction (MAR) were acquired for CIRT planning. MRI and MAR images were superimposed on the planning CT to delineate target volume and organs at risk. The radiation treatment plan consisted of a total dose of 51.6 Gy (relative biological effect) to be delivered in 12 fractions over 3 weeks, and the patient was irradiated in the supine and prone positions with a vertical beam, on alternating days. CIRT was completed as scheduled. No adverse events were observed during treatment or at 3 months after treatment initiation. While we show that CIRT may be a treatment option for patients with prostate cancer with bilateral hip prostheses, further studies are needed to evaluate treatment efficacy and late toxicity and to determine how CIRT can be administered to patients with prostate cancer with bilateral hip prostheses.

Evaluation of deformation parameters for deformable image registration-based ventilation imaging using an air-ventilating non-rigid phantom.

PURPOSE: This study aimed to evaluate different deformable image registration (DIR) parameters for the open-source NiftyReg package in its application to DIR-based ventilation imaging. METHODS: Two three-dimensional (3D)-computed tomography (CT) scans of a non-rigid air-ventilating phantom were acquired at peak exhalation and peak inhalation, with xenon (Xe) gas being used as an air-based contrast agent. We compared four different sets of DIR parameters, including one set with two-step deformation and three sets with four-step deformation. For spatial accuracy, the target registration error (TRE) was calculated for 16 landmarks. For ventilation imaging accuracy, DIR-based ventilation images were generated using Jacobian determinant (JD) metrics, and changes in Hounsfield unit (HU) values between the two exhalation and inhalation CT images were subsequently measured. The correlation coefficients between the JD metrics and changes in HU values were calculated. RESULTS: The mean TRE values were 4.5 ±â€¯4.7 mm (maximum, 12.3 mm), 1.47 ±â€¯0.71 mm (maximum, 2.6 mm), 1.56 ±â€¯0.70 mm (maximum, 2.8 mm), and 1.53 ±â€¯0.66 mm (maximum, 2.5 mm) for the two-step deformation and three four-step deformations, respectively. The four-step deformations (R =  - 0.71, -0.65, and -0.61) showed stronger correlation coefficients than the two-step deformation (R =  -0.40). CONCLUSIONS: The accuracy of DIR-based ventilation imaging may vary with different DIR parameter settings, even though spatial accuracy may be tolerable and within guidelines. We found adequate parameter settings for four-step NiftyReg DIR for visualization of simulated pulmonary ventilation function.

Design and development of a nonrigid phantom for the quantitative evaluation of DIR-based mapping of simulated pulmonary ventilation.

PURPOSE: The validation of deformable image registration (DIR)-based pulmonary ventilation mapping is time consuming and prone to inaccuracies and is also affected by deformation parameters. In this study, we developed a nonrigid phantom as a quality assurance (QA) tool that simulates ventilation to evaluate DIR-based images quantitatively. METHODS: The phantom consists of an acrylic cylinder filled with polyurethane foam designed to simulate pulmonic alveoli. A polyurethane membrane is attached to the inferior end of the phantom to simulate the diaphragm. In addition, tracheobronchial-tree-shaped polyurethane tubes are inserted through the foam and converge outside the phantom to simulate the trachea. Solid polyurethane is also used to model arteries, which closely follow the model airways. Two three-dimensional (3D) CT scans were performed during exhalation and inhalation phases using xenon (Xe) gas as the inhaled contrast agent. The exhalation 3D-CT image is deformed to an inhalation 3D-CT image using our in-house program based on the NiftyReg open-source package. The target registration error (TRE) between the two images was calculated for 16 landmarks located in the simulated lung volume. The DIR-based ventilation image was generated using Jacobian determinant (JD) metrics. Subsequently, differences in the Hounsfield unit (HU) values between the two images were measured. The correlation coefficient between the JD and HU differences was calculated. In addition, three 4D-CT scans are performed to evaluate the reproducibility of the phantom motion and Xe gas distribution. RESULTS: The phantom exhibited a variety of displacements for each landmark (range: 1-20 mm). The reproducibility analysis indicated that the location differences were <1 mm for all landmarks, and the HU variation in the Xe gas distribution was close to zero. The mean TRE in the evaluation of spatial accuracy according to the DIR software was 1.47 ± 0.71 mm (maximum: 2.6 mm). The relationship between the JD and HU differences had a large correlation (R = -0.71) for the DIR software. CONCLUSION: The phantom implemented new features, namely, deformation and simulated ventilation. To assess the accuracy of the DIR-based mapping of the simulated pulmonary ventilation, the phantom allows for simulation of Xe gas wash-in and wash-out. The phantom may be an effective QA tool, because the DIR algorithm can be quickly changed and its accuracy evaluated with a high degree of precision.

Alkaline-tolerant RNA aptamers useful to purify acid-sensitive antibodies in neutral conditions.

Recently, several oligonucleotides have been launched for clinical use and a number of therapeutic oligonucleotides are under clinical trials. Aptamer is one of the oligonucleotide therapeutics and has received a lot of attention as a new technology and an efficacious pharmaceutical compound comparable to antibody. Aptamer could be used for various purposes, not only therapeutics but also diagnostics, and applicable to affinity chromatography as a carrier molecule to purify proteins of interest. Here we demonstrate the usage and advantages of RNA aptamer to Fc region of human IgG (i.e., IgG aptamer) for purification of human antibodies. IgG aptamer requires divalent cations for binding to IgG and bound IgG dissociates easily upon treatment with chelating reagent, such as EDTA, under neutral conditions. This elution step is very mild and advantageous for maintaining active conformations of therapeutic antibodies compared to the widely used affinity purification with Protein A/G, which requires acidic elution that often damages the active conformation of antibodies. In fact, of several monoclonal antibodies tested, three antibodies were prone to aggregate on acidic elution from the Protein A/G resin, while remained fully active upon neutral elution from the IgG aptamer resin. The IgG aptamer was fully manipulated to alkaline resistant by ribose 2'-modifications, and thereby reusable numerous times with 1 N NaOH washing. The capacity of the aptamer resin to bind IgG was equivalent to that of the Protein A/G resin. Therefore, the IgG aptamer will provide us with a unique tool to uncover and purify human monoclonal antibodies, which hold therapeutic potential but lose the activity upon acidic elution from Protein A/G-based affinity resin.

Usefulness of a new online patient-specific quality assurance system for respiratory-gated radiotherapy.

PURPOSE: The accuracy of gated irradiation may decrease when treatment is performed with short "beam-on" times. Also, the dose is subject to variation between treatment sessions if the respiratory rate is irregular. We therefore evaluated the impact of the differences between gated and non-gated treatment on doses using a new online quality assurance (QA) system for respiratory-gated radiotherapy. METHODS: We generated dose estimation models to associate dose and pulse information using a 0.6 cc Farmer chamber and our QA system. During gated irradiation with each of seven regular and irregular respiratory patterns, with the Farmer chamber readings as references, we evaluated our QA system's accuracy. We then used the QA system to assess the impact of respiratory patterns on dose distribution for three lung and three liver radiotherapy plans. Gated and non-gated plans were generated and compared. RESULTS: There was agreement within 1.7% between the ionization chamber and our system for several regular and irregular motion patterns. For dose distributions with measured errors, there were larger differences between gated and non-gated treatment for high-dose regions within the planned treatment volume (PTV). Compared with a non-gated plan, PTV D95% for a gated plan decreased by -1.5% to -2.6%. Doses to organs at risk were similar with both plans. CONCLUSIONS: Our simple system estimated the radiation dose to the patient using only pulse information from the linac, even during irregular respiration. The quality of gated irradiation for each patient can be verified fraction by fraction.

NMR monitoring of the SELEX process to confirm enrichment of structured RNA.

RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 1015 different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed. In this study, we measured one-dimensional imino proton NMR spectra of RNA pools during SELEX. The spectrum of the initial RNA pool indicates that the RNAs adopt tertiary structures. The structural diversity of the RNA pools was shown to depend highly on the design of the primer-binding sequence. Furthermore, we demonstrate that enrichment of RNA aptamers can be monitored using NMR. The RNA pools can be recovered from the NMR tube after measurement of NMR spectra. We also can monitor target binding in the NMR tubes. Thus, we propose using NMR to monitor the enrichment of structured aptamers during the SELEX process.

Dual Therapeutic Action of a Neutralizing Anti-FGF2 Aptamer in Bone Disease and Bone Cancer Pain.

Fibroblast growth factor 2 (FGF2) plays a crucial role in bone remodeling and disease progression. However, the potential of FGF2 antagonists for treatment of patients with bone diseases has not yet been explored. Therefore, we generated a novel RNA aptamer, APT-F2, specific for human FGF2 and characterized its properties in vitro and in vivo. APT-F2 blocked binding of FGF2 to each of its four cellular receptors, inhibited FGF2-induced downstream signaling and cells proliferation, and restored osteoblast differentiation blocked by FGF2. APT-F2P, a PEGylated form of APT-F2, effectively blocked the bone disruption in mouse and rat models of arthritis and osteoporosis. Treatment with APT-F2P also exerted a strong analgesic effect, equivalent to morphine, in a mouse model of bone cancer pain. These findings demonstrated dual therapeutic action of APT-F2P in bone diseases and pain, providing a promising approach to the treatment of bone diseases.

Structural basis for specific inhibition of Autotaxin by a DNA aptamer.

ATX is a plasma lysophospholipase D that hydrolyzes lysophosphatidylcholine (LPC) and produces lysophosphatidic acid. To date, no ATX-inhibition-mediated treatment strategies for human diseases have been established. Here, we report anti-ATX DNA aptamers that inhibit ATX with high specificity and efficacy. We solved the crystal structure of ATX in complex with the anti-ATX aptamer RB011, at 2.0-Å resolution. RB011 binds in the vicinity of the active site through base-specific interactions, thus preventing the access of the choline moiety of LPC substrates. Using the structural information, we developed the modified anti-ATX DNA aptamer RB014, which exhibited in vivo efficacy in a bleomycin-induced pulmonary fibrosis mouse model. Our findings reveal the structural basis for the specific inhibition of ATX by the anti-ATX aptamer and highlight the therapeutic potential of anti-ATX aptamers for the treatment of human diseases, such as pulmonary fibrosis.

Midkine promotes neuroblastoma through Notch2 signaling.

Midkine is a heparin-binding growth factor highly expressed in various cancers, including neuroblastoma, the most common extracranial pediatric solid tumor. Prognosis of patients with neuroblastoma in which MYCN is amplified remains particularly poor. In this study, we used a MYCN transgenic model for neuroblastoma in which midkine is highly expressed in precancerous lesions of sympathetic ganglia. Genetic ablation of midkine in this model delayed tumor formation and reduced tumor incidence. Furthermore, an RNA aptamer that specifically bound midkine suppressed the growth of neuroblastoma cells in vitro and in vivo in tumor xenografts. In precancerous lesions, midkine-deficient MYCN transgenic mice exhibited defects in activation of Notch2, a candidate midkine receptor, and expression of the Notch target gene HES1. Similarly, RNA aptamer-treated tumor xenografts also showed attenuation of Notch2-HES1 signaling. Our findings establish a critical role for the midkine-Notch2 signaling axis in neuroblastoma tumorigenesis, which implicates new strategies to treat neuroblastoma.

RNA plasticity and selectivity applicable to therapeutics and novel biosensor development.

Aptamers are short, single-stranded nucleic acid sequences that are selected in vitro from large oligonucleotide libraries based on their high affinity to a target molecule. Hence, aptamers can be thought of as a nucleic acid analog to antibodies. However, several viewpoints hold that the potential of aptamers arises from interesting characteristics that are distinct from, or in some cases, superior to those of antibodies. This review summarizes the recent achievements in aptamer programs developed in our laboratory against basic and therapeutic protein targets. Through these studies, we became aware of the remarkable conformational plasticity and selectivity of RNA, on which the published report has not shed much light even though this is evidently a crucial feature for the strong specificity and affinity of RNA aptamers.

Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex.

Aptamers are short single-stranded nucleic acids with high affinity to target molecules and are applicable to therapeutics and diagnostics. Regardless of an increasing number of reported aptamers, the structural basis of the interaction of RNA aptamer with proteins is poorly understood. Here, we determined the 2.15 Å crystal structure of the Fc fragment of human IgG1 (hFc1) complexed with an anti-Fc RNA aptamer. The aptamer adopts a characteristic structure fit to hFc1 that is stabilized by a calcium ion, and the binding activity of the aptamer can be controlled many times by calcium chelation and addition. Importantly, the aptamer-hFc1 interaction involves mainly van der Waals contacts and hydrogen bonds rather than electrostatic forces, in contrast to other known aptamer-protein complexes. Moreover, the aptamer-hFc1 interaction involves human IgG-specific amino acids, rendering the aptamer specific to human IgGs, and not crossreactive to other species IgGs. Hence, the aptamer is a potent alternative for protein A affinity purification of Fc-fusion proteins and therapeutic antibodies. These results demonstrate, from a structural viewpoint, that conformational plasticity and selectivity of an RNA aptamer is achieved by multiple interactions other than electrostatic forces, which is applicable to many protein targets of low or no affinity to nucleic acids.

Crystallization and preliminary X-ray diffraction studies of an RNA aptamer in complex with the human IgG Fc fragment.

Aptamers, which are folded DNA or RNA molecules, bind to target molecules with high affinity and specificity. An RNA aptamer specific for the Fc fragment of human immunoglobulin G (IgG) has recently been identified and it has been demonstrated that an optimized 24-nucleotide RNA aptamer binds to the Fc fragment of human IgG and not to other species. In order to clarify the structural basis of the high specificity of the RNA aptamer, it was crystallized in complex with the Fc fragment of human IgG1. Preliminary X-ray diffraction studies revealed that the crystals belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 83.7, b = 107.2, c = 79.0 A. A data set has been collected to 2.2 A resolution.

Structural and molecular basis for hyperspecificity of RNA aptamer to human immunoglobulin G.

Potential applications for functional RNAs are rapidly expanding, not only to address functions based on primary nucleotide sequences, but also by RNA aptamer, which can suppress the activity of any target molecule. Aptamers are short DNA or RNA folded molecules that can be selected in vitro on the basis of their high affinity for a target molecule. Here, we demonstrate the ability of RNA aptamers to recognize--and bind to--human IgG with high specificity and affinity. An optimized 23-nucleotide aptamer, Apt8-2, was prepared, and was shown to bind to the Fc domain of human IgG, but not to other IgG's, with high affinity. Apt8-2 was observed to compete with protein A, but not with the Fcgamma receptor, for IgG binding. NMR chemical-shift analyses localized the aptamer-binding sites on the Fc subdomain, which partially overlaps the protein A binding site but not the Fcgamma receptor binding site. The tertiary structures of the predicted recognition sites on the Fc domain differ significantly between human IgG and other species of IgGs; this, in part, accounts for the high specificity of the selected aptamer. Apt8-2 can therefore be used as a protein A alternative for affinity purification of human IgG and therapeutic antibodies. Using Apt8-2 would have several potential advantages, raising the possibility of developing new applications based on aptamer design.

Inhibition of midkine alleviates experimental autoimmune encephalomyelitis through the expansion of regulatory T cell population.

CD4(+)CD25(+) regulatory T (Treg) cells are crucial mediators of autoimmune tolerance. The factors that regulate Treg cells, however, are largely unknown. Here, we show that deficiency in midkine (MK), a heparin-binding growth factor involved in oncogenesis, inflammation, and tissue repair, attenuated experimental autoimmune encephalomyelitis (EAE) because of an expansion of the Treg cell population in peripheral lymph nodes and decreased numbers of autoreactive T-helper type 1 (T(H)1) and T(H)17 cells. MK decreased the Treg cell population ex vivo in a dose-dependent manner by suppression of STAT5 phosphorylation that is essential for Foxp3 expression. Moreover, administration of anti-MK RNA aptamers significantly expanded the Treg cell population and alleviated EAE symptoms. These observations indicate that MK serves as a critical suppressor of Treg cell expansion, and inhibition of MK using RNA aptamers may provide an effective therapeutic strategy against autoimmune diseases, including multiple sclerosis.

Studies in the mineral and salt-catalyzed formation of RNA oligomers.

Activated mononucleotides oligomerize in the presence of montmorillonite clay to form RNA oligomers. In the present study, effects of salts, temperature and pH on the clay-catalyzed synthesis of RNA oligomers were investigated. This reaction is favored by relatively high concentration of salts, such as 1 M NaCl. It was shown that the presence of divalent cations was not required for this reaction. High concentrations of NH4+ and HCO3- and 0.01 M HPO4(2-) inhibit the reaction. The yields of RNA oligomers decreased as the temperature was raised from 4 degrees C to 50 degrees C. A5' ppA was the major product at pH's below 6. The catalytic activity of a variety of minerals and three meteorites were investigated but none of them except galena catalyzed the oligomerization. ATP was generated from ADP but it was due to the presence of HEPES buffer and not due to the minerals. Meteorites catalyzed the hydrolysis of the pyrophosphate bonds of ATP. The results suggest that oligomers of RNA could have formed in pH 7-9 solutions of alkali metal salts in the presence of montmorillonite clay.