Evaluation of saliva as a source of accurate whole-genome and microbiome sequencing data.

This study sets out to establish the suitability of saliva-based whole-genome sequencing (WGS) through a comparison against blood-based WGS. To fully appraise the observed differences, we developed a novel technique of pseudo-replication. We also investigated the potential of characterizing individual salivary microbiomes from non-human DNA fragments found in saliva. We observed that the majority of discordant genotype calls between blood and saliva fell into known regions of the human genome that are typically sequenced with low confidence; and could be identified by quality control measures. Pseudo-replication demonstrated that the levels of discordance between blood- and saliva-derived WGS data were entirely similar to what one would expect between technical replicates if an individual's blood or saliva had been sequenced twice. Finally, we successfully sequenced salivary microbiomes in parallel to human genomes as demonstrated by a comparison against the Human Microbiome Project.

Feasibility of high-throughput sequencing in clinical routine cancer care: lessons from the cancer pilot project of the France Genomic Medicine 2025 plan.

BACKGROUND: Whole exome sequencing and RNA sequencing (WES/RNASeq) should now be implemented in the clinical practice in order to increase access to optimal care for cancer patients. Providing results to Tumour Boards in a relevant time frame-that is, compatible with the clinical pathway-is crucial. Assessing the feasibility of this implementation in the French care system is the primary objective of the Multipli study, as one of the four pilot projects of the national France Genomic Medicine 2025 (FGM 2025) plan. The Multipli study encompasses two innovative trials which will be driven in around 2400 patients suffering from a soft-tissue sarcoma (Multisarc) or a metastatic colorectal carcinoma (Acompli). METHODS: Prior to launching the FGM 2025 cancer pilot study itself, the performance of the Multipli genomic workflow has been evaluated through each step, from the samples collection to the Molecular Tumour Board (MTB) report. Two Multipli-assigned INCa-labelled molecular genetics centres, the CEA-CNRGH sequencing platform and the Institut Bergonié's Bioinformatics Platform were involved in a multicentric study. The duration of each step of the genomic workflow was monitored and bottlenecks were identified. RESULTS: Thirty barriers which could affect the quality of the samples, sequencing results and the duration of each step of the genomic pathway were identified and mastered. The global turnaround time from the sample reception to the MTB report was of 44 calendar days. CONCLUSION: Our results demonstrate the feasibility of tumour genomic analysis by WES/RNASeq within a time frame compatible with the current cancer patient care. Lessons learnt from the Multipli WES/RNASeq Platforms Workflow Study will constitute guidelines for the forthcoming Multipli study and more broadly for the future clinical routine practice in the first two France Genomic Medicine 2025 platforms.

Magnetosomes, biogenic magnetic nanomaterials for brain molecular imaging with 17.2 T MRI scanner.

The fast development of sensitive molecular diagnostic tools is currently paving the way for a personalized medicine. A new class of ultrasensitive magnetic resonance imaging (MRI) T2-contrast agents based on magnetosomes, magnetite nanocrystals biomineralized by magnetotactic bacteria, is proposed here. The contrast agents can be injected into the blood circulation and detected in the picomolar range. Purified magnetosomes are water-dispersible and stable within physiological conditions and exhibit at 17.2 T a transverse relaxivity r2 four times higher than commercial ferumoxide. The subsequent gain in sensitivity by T2(*) -weighted imaging at 17.2 T of the mouse brain vasculature is evidenced in vivo after tail vein injection of magnetosomes representing a low dose of iron (20 µmoliron kg(-1)), whereas no such phenomenon with the same dose of ferumoxide is observed. Preclinical studies of human pathologies in animal models will benefit from the combination of high magnetic field MRI with sensitive, low dose, easy-to-produce biocompatible contrast agents derived from bacterial magnetosomes.

In vivo CEST MR imaging of U87 mice brain tumor angiogenesis using targeted LipoCEST contrast agent at 7 T.

LipoCEST are liposome-encapsulating paramagnetic contrast agents (CA) based on chemical exchange saturation transfer with applications in biomolecular MRI. Their attractive features include biocompatibility, subnanomolar sensitivity, and amenability to functionalization for targeting biomarkers. We demonstrate MR imaging using a targeted lipoCEST, injected intravenously. A lipoCEST carrying Tm(III)-complexes was conjugated to RGD tripeptide (RGD-lipoCEST), to target integrin α(ν)ß(3) receptors involved in tumor angiogenesis and was compared with an unconjugated lipoCEST. Brain tumors were induced in athymic nude mice by intracerebral injection of U87MG cells and were imaged at 7 T after intravenous injection of either of the two contrast agents (n = 12 for each group). Chemical exchange saturation transfer-MSME sequence was applied over 2 h with an average acquisition time interval of 13.5 min. The chemical exchange saturation transfer signal was ∼1% in the tumor and controlateral regions, and decreased to ∼0.3% after 2 h; while RGD-lipoCEST signal was ∼1.4% in the tumor region and persisted for up to 2 h. Immunohistochemical staining revealed a persistent colocalization of RGD-lipoCEST with α(ν)ß(3) receptors in the tumor region. These results constitute an encouraging step toward in vivo MRI imaging of tumor angiogenesis using intravenously injected lipoCEST.

19F molecular MR imaging for detection of brain tumor angiogenesis: in vivo validation using targeted PFOB nanoparticles.

Molecular imaging with magnetic resonance imaging (MRI) targeted contrast agents has emerged as a promising diagnostic approach in cancer research to detect associated biomarkers. In this work, the potential of (19)F MRI was investigated to detect angiogenesis with α(ν)ß(3)-targeted perfluorooctylbromide nanoparticles (PFOB NP) in a U87 glioblastoma mouse model at 7 Tesla. Mice were injected intravenously with targeted or non-targeted NP and (19)F images were immediately acquired for 90 min using a PFOB-dedicated MRI sequence. Mice infused with targeted NP exhibited higher concentrations in tumors than mice of the control group, despite the presence of nonspecific signal originating from the blood. Imaging results were corroborated by histology and fluorescence imaging, suggesting specific binding of targeted NP to α(ν)ß(3) integrin. Two other groups of mice were injected 24 h before imaging to allow blood clearance but no significant differences were found between both groups, probably due to a loss of specificity of PFOB NP. This is the first demonstration of the ability of (19)F MRI to detect α(ν)ß(3)-integrin endothelial expression in brain tumors in vivo.

Dynamic study of blood-brain barrier closure after its disruption using ultrasound: a quantitative analysis.

Delivery of therapeutic or diagnostic agents to the brain is majorly hindered by the blood-brain barrier (BBB). Recently, many studies have demonstrated local and transient disruption of the BBB using low power ultrasound sonication combined with intravascular microbubbles. However, BBB opening and closure mechanisms are poorly understood, especially the maximum gap that may be safely generated between endothelial cells and the duration of opening of the BBB. Here, we studied BBB opening and closure under magnetic resonance (MR) guidance in a rat model. First, MR contrast agents (CA) of different hydrodynamic diameters (1 to 65 nm) were employed to estimate the largest molecular size permissible across the cerebral tissues. Second, to estimate the duration of the BBB opening, the CA were injected at various times post-BBB disruption (12 minutes to 24 hours). A T(1) mapping strategy was developed to assess CA concentration at the ultrasound (US) focal point. Based on our experimental data and BBB closure modeling, a calibration curve was obtained to compute the half closure time as a function of CA hydrodynamic diameter. These findings and the model provide an invaluable basis for optimal design and delivery of nanoparticles to the brain.

A new sequence for single-shot diffusion-weighted NMR spectroscopy by the trace of the diffusion tensor.

Diffusion-weighted spectroscopy is a unique tool for exploring the intracellular microenvironment in vivo. In living systems, diffusion may be anisotropic, when biological membranes exhibit particular orientation patterns. In this work, a volume selective diffusion-weighted sequence is proposed, allowing single-shot measurement of the trace of the diffusion tensor, which does not depend on tissue anisotropy. With this sequence, the minimal echo time is only three times the diffusion time. In addition, cross-terms between diffusion gradients and other gradients are cancelled out. An adiabatic version, similar to localization by adiabatic selective refocusing sequence, is then derived, providing partial immunity against cross-terms. Proof of concept is performed ex vivo on chicken skeletal muscle by varying tissue orientation and intra-voxel shim. In vivo performance of the sequence is finally illustrated in a U87 glioblastoma mouse model, allowing the measurement of the trace apparent diffusion coefficient for six metabolites, including J-modulated metabolites. Although measurement performed along three separate orthogonal directions would bring similar accuracy on trace apparent diffusion coefficient under ideal conditions, the method described here should be useful for probing intimate properties of the cells with minimal experimental bias.

High sensitivity 19F MRI of a perfluorooctyl bromide emulsion: application to a dynamic biodistribution study and oxygen tension mapping in the mouse liver and spleen.

We have recently developed an optimized multi-spin echo (MSE) sequence dedicated to perfluorooctyl bromide (PFOB) imaging yielding an excellent sensitivity in vitro. The aim of the present study was to apply this sequence to quantitative measurements in the mouse liver and spleen after intravenous (i.v.) injection of PFOB emulsions. We first performed oxygenation maps 25.5 min after a single infusion of emulsion and, contrary to previous studies, shortly after injection. The signal-to-noise ratio (SNR) in the liver and spleen was as high as 45 and 120, respectively, for 3-min images with 11.7-µL pixels. Values of oxygen tension tended to be slightly higher in the spleen than in the liver. Dynamic biodistribution experiments were then performed immediately after intravenous (i.v.) injection of PFOB emulsions grafted with different quantities of polyethylene glycol (PEG) for stealth. Images were acquired every 7 min for 84 min and the SNR measured in the liver and spleen was at least four from the first time point. Uptake rates could be assessed for each PEG amount and, in spite of high standard deviations (SDs) owing to interanimal variability, our data confirmed that increasing quantities of PEG allow more gradual uptake of the emulsion particles by the liver and spleen. In conclusion, our method seems to be a powerful tool to non-invasively perform accurate in vivo quantitative measurements in the liver and spleen using (19)F MRI.

About the origins of NMR diffusion-weighting induced by frequency-swept pulses.

In the present work, the non-linear phase dispersion induced by slice selective frequency-swept pulses is analyzed, in order to assess NMR signal attenuation due to molecular diffusion during such pulses. In particular, theoretical considerations show that diffusion-weighting can be calculated based on the non-linear phase spatial derivative (i.e. the phase gradient), and that the phase of B(1) field at the instant of the flip does not contribute to phase scrambling and diffusion-weighting, yielding a simple analytical expressions. The theory is validated by confrontation with numerical simulations of the Bloch equations including diffusion, performed for a pair of hyperbolic secant pulses and a pair of CHIRP pulses. The simple though general conceptual framework developed here should be useful for the understanding and the exact calculation of diffusion-weighting in NMR sequences using frequency-swept pulses.

A new paradigm for high-sensitivity 19F magnetic resonance imaging of perfluorooctylbromide.

In the present work, the NMR properties of perfluorooctylbromide are revisited to derive a high-sensitivity fluorine MRI strategy. It is shown that the harmful effects of J-coupling can be eliminated by carefully choosing the bandwidth of the 180 degrees pulses in a spin-echo sequence. The T(2) of the CF(3) resonance of the molecule is measured using a multispin-echo sequence and shown to dramatically depend on the interpulse delay. Following these observations, an optimized multispin-echo imaging sequence is derived and compared with short TE/pulse repetition time gradient echo and chemical shift imaging sequences. The unparalleled sensitivity yielded by the multispin-echo sequence is promising for future applications, in particular for targeted contrast agents such as perfluorooctylbromide nanoparticles.

Artifacts and pitfalls in diffusion MRI.

Although over the last 20 years diffusion MRI has become an established technique with a great impact on health care and neurosciences, like any other MRI technique it remains subject to artifacts and pitfalls. In addition to common MRI artifacts, there are specific problems that one may encounter when using MRI scanner gradient hardware for diffusion MRI, especially in terms of eddy currents and sensitivity to motion. In this article we review those artifacts and pitfalls on a qualitative basis, and introduce possible strategies that have been developed to mitigate or overcome them.

Frequency-shift based detection of BMS contrast agents using SSFP: potential for MRA.

A novel mechanism of MRI contrast enhancement, based on the detection by a balanced steady-state free precession (SSFP) sequence of the proton resonance frequency shift induced by bulk magnetic susceptibility (BMS) contrast agents, was investigated. The potential for this contrast mechanism to image blood vessels was explored. The relaxation time and the frequency shift effects of gadolinium- and dysprosium-DOTA on SSFP signal was first simulated and evaluated on a water phantom at 1.5 T. In vitro, a 5-mM concentration in contrast agent induced a 20-Hz frequency shift, leading to a signal increase of 92% for Dy-DOTA, and a 10-Hz frequency shift, leading to a signal increase of 58% for Gd-DOTA at the reference frequency, taking into account the nonlinear SSFP signal response on frequency offset. The concept was then evaluated in vivo on anesthetized rabbits. Low doses of dysprosium-DOTA were injected in their vascular system, and imaging was performed at the level of neck vessels. Following a bolus injection, mean signal changes of 31%, 20% and 14% were observed in the carotid arteries, the vertebral veins and the jugular veins, respectively. The bolus peak times in arteries and veins were consistent with the rabbit vascular circulation. This frequency-shift based contrast mechanism presents interesting potential for contrast-enhanced MR angiography (CE-MRA) compared to usual relaxation-based contrast, but further investigations on reproducibility will be necessary.

Use of fast spin echo for phase shift magnetic resonance thermometry.

PURPOSE: To propose a modified fast spin echo (FSE) magnetic resonance imaging sequence for MR thermometry, employing the proton resonance frequency (PRF) shift by means of MR phase maps. Despite their obvious advantages of speed and high signal-to-noise ratio (SNR), FSE sequences have not until now been used for this purpose due to the restraints imposed by the Carr-Purcell-Meiboom-Gill (CPMG) conditions. MATERIALS AND METHODS: The new FSE combines a new phase modulation scheme that maintains magnetization that ordinarily is destroyed under CPMG conditions, while employing conventional FSE gradient waveforms. The echoes are read in a single shot using 128 readouts in 650 msec, with a phase sensitive preparation using an optional time shift tau before the start of the refocusing gradient waveforms. This feature allows the quantification of temperature dependent phase shifts. We tested the sequence by imaging a heated agar gel phantom while cooling, using different values for tau. RESULTS: There was good correlation between FSE and fiberoptic-based temperature measurements in the phantom(r(2) >or= 0.95). Temperature sensitivity could be adjusted by varying the tau value. CONCLUSION: With the proposed non-CPMG FSE sequence it is feasible to quantify temperature changes by means of the PRF shift.

Interventional MR imaging at 1.5 T: quantification of sound exposure.

Sound pressure levels (SPLs) during interventional magnetic resonance (MR) imaging may create an occupational hazard for the interventional radiologist (ie, the potential risk of hearing impairment). Therefore, A-weighted and linear continuous-equivalent SPLs were measured at the entrance of a 1.5-T MR imager during cardiovascular and real-time pulse sequences. The SPLs ranged from 81.5 to 99.3 dB (A-weighted scale), and frequencies were from 1 to 3 kHz. SPLs for the interventional radiologist exceeded a safe SPL of 80 dB (A-weighted scale) for all sequences; therefore, hearing protection is recommended.

Evaluation of a dedicated dual phased-array surface coil using a black-blood FSE sequence for high resolution MRI of the carotid vessel wall.

PURPOSE: To investigate the ability of magnetic resonance imaging (MRI) to visualize the carotid vessel wall using a phased-array coil and a black-blood (BB) fast spin-echo (FSE) sequence. MATERIALS AND METHODS: The phased-array coil was compared with a three-inch coil. Images from volunteers were evaluated for artifacts, wall layers, and wall signal intensity. Signal intensity and homogeneity of atherosclerosis were assessed. Lumen diameter and vessel area were measured. RESULTS: Comparison between the phased-array coil and the three-inch coil showed a 100% increase in signal-to-noise ratio. BB-FSE imaging resulted in good delineation between blood and vessel wall. Most volunteers had a two-layered vessel wall with a hyperintense inner layer. MRI showed both homogeneous hyperintense and heterogeneous plaques, which consisted of a main hyperintense part with hypointense spots and/or intermediate regions. MRI lumen and area measurements were performed easily. CONCLUSION: High resolution MRI of carotid atherosclerosis is feasible with a phased-array coil and a BB-FSE sequence.