Abstract
pH alterations are a hallmark of many pathologies including cancer and kidney disease. Here, we introduce 1,5-
13
C
2
Z-OMPD as a hyperpolarized extracellular pH and perfusion sensor for MRI ...which allows to generate a multiparametric fingerprint of renal disease status and to detect local tumor acidification. Exceptional long T
1
of two minutes at 1 T, high pH sensitivity of up to 1.9 ppm per pH unit and suitability of using the C
1
-label as internal frequency reference enables pH imaging in vivo of three pH compartments in healthy rat kidneys. Spectrally selective targeting of both
13
C-resonances enables simultaneous imaging of perfusion and filtration in 3D and pH in 2D within one minute to quantify renal blood flow, glomerular filtration rates and renal pH in healthy and hydronephrotic kidneys with superior sensitivity compared to clinical routine methods. Imaging multiple biomarkers within a single session renders 1,5-
13
C
2
Z-OMPD a promising new hyperpolarized agent for oncology and nephrology.
Human T-lymphotropic virus type 1 (HTLV-1) is a retrovirus that persists lifelong in the host. In ∼4% of infected people, HTLV-1 causes a chronic disabling neuroinflammatory disease known as ...HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The pathogenesis of HAM/TSP is unknown and treatment remains ineffective. We used gene expression microarrays followed by flow cytometric and functional assays to investigate global changes in blood transcriptional profiles of HTLV-1-infected and seronegative individuals. We found that perturbations of the p53 signaling pathway were a hallmark of HTLV-1 infection. In contrast, a subset of interferon (IFN)-stimulated genes was over-expressed in patients with HAM/TSP but not in asymptomatic HTLV-1 carriers or patients with the clinically similar disease multiple sclerosis. The IFN-inducible signature was present in all circulating leukocytes and its intensity correlated with the clinical severity of HAM/TSP. Leukocytes from patients with HAM/TSP were primed to respond strongly to stimulation with exogenous IFN. However, while type I IFN suppressed expression of the HTLV-1 structural protein Gag it failed to suppress the highly immunogenic viral transcriptional transactivator Tax. We conclude that over-expression of a subset of IFN-stimulated genes in chronic HTLV-1 infection does not constitute an efficient host response but instead contributes to the development of HAM/TSP.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Gene set analysis methods, which consider predefined groups of genes in the analysis of genomic data, have been successfully applied for analyzing gene expression data in cross-sectional studies. The ...time-course gene set analysis (TcGSA) introduced here is an extension of gene set analysis to longitudinal data. The proposed method relies on random effects modeling with maximum likelihood estimates. It allows to use all available repeated measurements while dealing with unbalanced data due to missing at random (MAR) measurements. TcGSA is a hypothesis driven method that identifies a priori defined gene sets with significant expression variations over time, taking into account the potential heterogeneity of expression within gene sets. When biological conditions are compared, the method indicates if the time patterns of gene sets significantly differ according to these conditions. The interest of the method is illustrated by its application to two real life datasets: an HIV therapeutic vaccine trial (DALIA-1 trial), and data from a recent study on influenza and pneumococcal vaccines. In the DALIA-1 trial TcGSA revealed a significant change in gene expression over time within 69 gene sets during vaccination, while a standard univariate individual gene analysis corrected for multiple testing as well as a standard a Gene Set Enrichment Analysis (GSEA) for time series both failed to detect any significant pattern change over time. When applied to the second illustrative data set, TcGSA allowed the identification of 4 gene sets finally found to be linked with the influenza vaccine too although they were found to be associated to the pneumococcal vaccine only in previous analyses. In our simulation study TcGSA exhibits good statistical properties, and an increased power compared to other approaches for analyzing time-course expression patterns of gene sets. The method is made available for the community through an R package.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Whole blood transcriptional profiling offers great diagnostic and prognostic potential. Although studies identified signatures for pulmonary tuberculosis (TB) and transcripts that predict the risk ...for developing active TB in humans, the early transcriptional changes immediately following Mycobacterium tuberculosis infection have not been evaluated. We evaluated the gene expression changes in the cynomolgus macaque model of TB, which recapitulates all clinical aspects of human M. tuberculosis infection, using a human microarray and analytics platform. We performed genome-wide blood transcriptional analysis on 38 macaques at 11 postinfection time points during the first 6 mo of M. tuberculosis infection. Of 6371 differentially expressed transcripts between preinfection and postinfection, the greatest change in transcriptional activity occurred 20-56 d postinfection, during which fluctuation of innate and adaptive immune response-related transcripts was observed. Modest transcriptional differences between active TB and latent infection were observed over the time course with substantial overlap. The pattern of module activity previously published for human active TB was similar in macaques with active disease. Blood transcript activity was highly correlated with lung inflammation (lung
Ffluorodeoxyglucose FDG avidity) measured by positron emission tomography and computed tomography at early time points postinfection. The differential signatures between animals with high and low lung FDG were stronger than between clinical outcomes. Analysis of preinfection signatures of macaques revealed that IFN signatures could influence eventual clinical outcomes and lung FDG avidity, even before infection. Our data support that transcriptional changes in the macaque model are translatable to human M. tuberculosis infection and offer important insights into early events of M. tuberculosis infection.
To develop a high spatiotemporal resolution 3D dynamic pulse sequence for preclinical imaging of hyperpolarized 1-
Cpyruvate-to-1-
Clactate metabolism at 7T.
A standard 3D balanced SSFP (bSSFP) ...sequence was modified to enable alternating-frequency excitations. RF pulses with 2.33 ms duration and 900 Hz FWHM were placed off-resonance of the target metabolites, 1-
Cpyruvate (by approximately -245 Hz) and 1-
Clactate (by approximately 735 Hz), to selectively excite those resonances. Relatively broad bandwidth (compared to those metabolites' chemical shift offset) permits a short TR of 6.29 ms, enabling higher spatiotemporal resolution. Bloch equation simulations of the bSSFP response profile guided the sequence parameter selection to minimize spectral contamination between metabolites and preserve magnetization over time.
Bloch equation simulations, phantom studies, and in vivo studies demonstrated that the two target resonances could be cleanly imaged without substantial bSSFP banding artifacts and with little spectral contamination between lactate and pyruvate and from pyruvate hydrate. High spatiotemporal resolution 3D images were acquired of in vivo pyruvate-lactate metabolism in healthy wild-type and endogenous pancreatic tumor-bearing mice, with 1.212 s acquisition time per single-metabolite image and (1.75 mm)
isotropic voxels with full mouse abdomen 56 × 28 × 21 mm
FOV and fully-sampled k-space. Kidney and tumor lactate/pyruvate ratios of two consecutive measurements in one animal, 1 h apart, were consistent.
Spectrally selective bSSFP using off-resonant RF excitations can provide high spatio-temporal resolution 3D dynamic images of pyruvate-lactate metabolic conversion.
Hyperpolarization is an emerging method in magnetic resonance imaging that allows nuclear spin polarization of gases or liquids to be temporarily enhanced by up to five or six orders of magnitude at ...clinically relevant field strengths and administered at high concentration to a subject at the time of measurement. This transient gain in signal has enabled the non-invasive detection and imaging of gas ventilation and diffusion in the lungs, perfusion in blood vessels and tissues, and metabolic conversion in cells, animals, and patients. The rapid development of this method is based on advances in polarizer technology, the availability of suitable probe isotopes and molecules, improved MRI hardware and pulse sequence development. Acquisition strategies for hyperpolarized nuclei are not yet standardized and are set up individually at most sites depending on the specific requirements of the probe, the object of interest, and the MRI hardware. This review provides a detailed introduction to spatially resolved detection of hyperpolarized nuclei and summarizes novel and previously established acquisition strategies for different key areas of application.
Background
Anti‐IgE (omalizumab) has been used for the treatment of moderate‐to‐severe asthma that is not controlled by inhaled steroids. Despite its success, it does not always provide patients with ...significant clinical benefits.
Objective
To investigate the transcriptional variations between omalizumab responders and non‐responders and to study the mechanisms of action of omalizumab.
Methods
The whole blood transcriptomes of moderate‐to‐severe adult asthma patients (N = 45:34 responders and 11 non‐responders) were analysed over the course of omalizumab treatment. Non‐asthmatic healthy controls (N = 17) were used as controls.
Results
Transcriptome variations between responders and non‐responders were identified using the genes significant (FDR < 0.05) in at least one comparison of each patient response status and time point compared with control subjects. Using gene ontology and network analysis, eight clusters of genes were identified. Longitudinal analyses of individual clusters revealed that responders could maintain changes induced with omalizumab treatment and become more similar to the control subjects, while non‐responders tend to remain more similar to their pre‐treatment baseline. Further analysis of an inflammatory gene cluster revealed that genes associated with neutrophil/eosinophil activities were up‐regulated in non‐responders and, more importantly, omalizumab did not significantly alter their expression levels. The application of modular analysis supported our findings and further revealed variations between responders and non‐responders.
Conclusion and Clinical Relevance
This study provides not only transcriptional variations between omalizumab responders and non‐responders, but also molecular insights for controlling asthma by omalizumab.
Background
Hyperpolarization enhances the sensitivity of nuclear magnetic resonance experiments by between four and five orders of magnitude. Several hyperpolarized sensor molecules have been ...introduced that enable high sensitivity detection of metabolism and physiological parameters. However, hyperpolarized magnetic resonance spectroscopy imaging (MRSI) often suffers from poor signal-to-noise ratio and spectral analysis is complicated by peak overlap. Here, we study measurements of extracellular pH (pH
e
) by hyperpolarized zymonic acid, where multiple pH
e
compartments, such as those observed in healthy kidney or other heterogeneous tissue, result in a cluster of spectrally overlapping peaks, which is hard to resolve with conventional spectroscopy analysis routines.
Methods
We investigate whether deep learning methods can yield improved pH
e
prediction in hyperpolarized zymonic acid spectra of multiple pH
e
compartments compared to conventional line fitting. As hyperpolarized
13
C-MRSI data sets are often small, a convolutional neural network (CNN) and a multilayer perceptron (MLP) were trained with either a synthetic or a mixed (synthetic and augmented) data set of acquisitions from the kidneys of healthy mice.
Results
Comparing the networks’ performances compartment-wise on a synthetic test data set and eight real kidney data shows superior performance of CNN compared to MLP and equal or superior performance compared to conventional line fitting. For correct prediction of real kidney pH
e
values, training with a mixed data set containing only 0.5% real data shows a large improvement compared to training with synthetic data only. Using a manual segmentation approach, pH maps of kidney compartments can be improved by neural network predictions for voxels including three pH compartments.
Conclusion
The results of this study indicate that CNNs offer a reliable, accurate, fast and non-interactive method for analysis of hyperpolarized
13
C MRS and MRSI data, where low amounts of acquired data can be complemented to achieve suitable network training.
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•Standard models of SEOP describe the high Xe density, high photon flux regime.•A laser power and Xe density independent ‘optimal absorption’ is reported.•A simulation guided roadmap ...for increasing clinical scale Xe polariser performance.
Spin-exchange optical pumping (SEOP) can enhance the NMR sensitivity of noble gases by up to five orders of magnitude at Tesla-strength magnetic fields. SEOP-generated hyperpolarised (HP) 129Xe is a promising contrast agent for lung imaging but an ongoing barrier to widespread clinical usage has been economical production of sufficient quantities with high 129Xe polarisation. Here, the ‘standard model’ of SEOP, which was previously used in the optimisation of continuous-flow 129Xe polarisers, is modified for validation against two Xe-rich stopped-flow SEOP datasets. We use this model to examine ways to increase HP Xe production efficiency in stopped-flow 129Xe polarisers and provide further insight into the underlying physics of Xe-rich stopped-flow SEOP at high laser fluxes.
The aim of this study was to acquire the transient MRI signal of hyperpolarized tracers and their metabolites efficiently, for which specialized imaging sequences are required. In this work, a ...multi‐echo balanced steady‐state free precession (me‐bSSFP) sequence with Iterative Decomposition with Echo Asymmetry and Least squares estimation (IDEAL) reconstruction was implemented on a clinical 3 T positron‐emission tomography/MRI system for fast 2D and 3D metabolic imaging. Simulations were conducted to obtain signal‐efficient sequence protocols for the metabolic imaging of hyperpolarized biomolecules. The sequence was applied in vitro and in vivo for probing the enzymatic exchange of hyperpolarized 1–13Cpyruvate and 1–13Clactate. Chemical shift resolution was achieved using a least‐square, iterative chemical species separation algorithm in the reconstruction. In vitro, metabolic conversion rate measurements from me‐bSSFP were compared with NMR spectroscopy and free induction decay‐chemical shift imaging (FID‐CSI). In vivo, a rat MAT‐B‐III tumor model was imaged with me‐bSSFP and FID‐CSI. 2D metabolite maps of 1–13Cpyruvate and 1–13Clactate acquired with me‐bSSFP showed the same spatial distributions as FID‐CSI. The pyruvate‐lactate conversion kinetics measured with me‐bSSFP and NMR corresponded well. Dynamic 2D metabolite mapping with me‐bSSFP enabled the acquisition of up to 420 time frames (scan time: 180‐350 ms/frame) before the hyperpolarized 1–13Cpyruvate was relaxed below noise level. 3D metabolite mapping with a large field of view (180 × 180 × 48 mm3) and high spatial resolution (5.6 × 5.6 × 2 mm3) was conducted with me‐bSSFP in a scan time of 8.2 seconds. It was concluded that Me‐bSSFP improves the spatial and temporal resolution for metabolic imaging of hyperpolarized 1–13Cpyruvate and 1–13Clactate compared with either of the FID‐CSI or EPSI methods reported at 3 T, providing new possibilities for clinical and preclinical applications.
2D and 3D dynamic hyperpolarized 13C MR spectroscopic imaging were conducted at 3 T using a multi‐echo balanced steady‐state free precession sequence and Iterative Decomposition with Echo Asymmetry and Least squares estimation reconstruction. The sequence was specialized to image pyruvate to lactate conversion with high temporal and spatial resolution in vitro and in vivo. High SNR, improved resolution in shorter scan time and more efficient usage of the magnetization was found compared with a free induction decay‐chemical shift imaging sequence.
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