Accelerated 3D multi-echo spin-echo sequence with a subspace constrained reconstruction for whole mouse brain T 2 mapping.

PURPOSE: To accelerate whole-brain quantitative T 2 $$ {\mathrm{T}}_2 $$ mapping in preclinical imaging setting. METHODS: A three-dimensional (3D) multi-echo spin echo sequence was highly undersampled with a variable density Poisson distribution to reduce the acquisition time. Advanced iterative reconstruction based on linear subspace constraints was employed to recover high-quality raw images. Different subspaces, generated using exponential or extended-phase graph (EPG) simulations or from low-resolution calibration images, were compared. The subspace dimension was investigated in terms of T 2 $$ {\mathrm{T}}_2 $$ precision. The method was validated on a phantom containing a wide range of T 2 $$ {\mathrm{T}}_2 $$ and was then applied to monitor metastasis growth in the mouse brain at 4.7T. Image quality and T 2 $$ {\mathrm{T}}_2 $$ estimation were assessed for 3 acceleration factors (6/8/10). RESULTS: The EPG-based dictionary gave robust estimations of a large range of T 2 $$ {\mathrm{T}}_2 $$ . A subspace dimension of 6 was the best compromise between T 2 $$ {\mathrm{T}}_2 $$ precision and image quality. Combining the subspace constrained reconstruction with a highly undersampled dataset enabled the acquisition of whole-brain T 2 $$ {\mathrm{T}}_2 $$ maps, the detection and the monitoring of metastasis growth of less than 500 µ m 3 $$ \mu {\mathrm{m}}^3 $$ . CONCLUSION: Subspace-based reconstruction is suitable for 3D T 2 $$ {\mathrm{T}}_2 $$ mapping. This method can be used to reach an acceleration factor up to 8, corresponding to an acquisition time of 25 min for an isotropic 3D acquisition of 156 µ $$ \mu $$ m on the mouse brain, used here for monitoring metastases growth.

New setup for multi-parametric MRI in young and old rat gastrocnemius at 4.7 and 7 T during muscle stimulation.

T1 and T2 relaxation times combined with 31 P spectroscopy have been proven efficient for muscular disease characterization as well as for pre- and post-muscle stimulation measurements. Even though 31 P spectroscopy can already be performed during muscle exercise, no method for T1 and T2 measurement enables this possibility. In this project, a complete setup and protocol for multi-parametrical MRI of the rat gastrocnemius before, during and after muscle stimulation at 4.7 and 7 T is presented. The setup is fully MRI compatible and is composed of a cradle, an electro-stimulator and an electronic card in order to synchronize MRI sequences with muscle stimulation. A 2D triggered radial-encoded Look-Locker sequence was developed, and enabled T1 measurements in less than 2 min on stimulated muscle. Also, a multi-slice multi-echo sequence was adapted and synchronized for T2 measurements as well as 31 P spectroscopy acquisitions in less than 4 min in both cases on stimulated muscle. Methods were validated on young rats using different stimulation paradigms. Then they were applied on older rats to compare quantification results, using the different stimulation paradigms, and allowed observation of metabolic changes related to aging with good reproducibility. The robustness of the whole setup shows wide application opportunities.

Three-dimensional ultrashort echo time (3D UTE) magnetic resonance imaging (MRI) of the normal and degenerative disco-vertebral complex at 4.7 T: a feasibility study with longitudinal evaluation.

OBJECTIVES: To assess feasibility of a three-dimensional ultrashort echo time (3D-UTE)-sequence to evaluate normal and pathological disco-vertebral complex (DVC), with assessment of its different portions in a rat model of degenerative disk disease (DDD) with histological correlation. To assess whether this sequence, in comparison with long echo time T2-weighted sequence, is able to monitor DDD with differentiation of early from chronic DVC changes in pathological mechanical conditions. METHODS: Five rats were induced with DDD model by percutaneous disk trituration of the tail with an 18-G needle under US-guidance and imaged at 4.7 T. MRI protocol included fat-saturated-T2 (RARE) and 3D-UTE-sequences performed at baseline (day 0. n = 5 animals /10 DVC) and each week (W) from W1 to W10 postoperatively. Visual analysis and signal intensity measurements of SNR and CNR of all DVC portions were performed on RARE and UTE images. Following killing (baseline, n = 1/2 DVC; W2, n = 2/4 DVC; W10, n = 2/4 DVC), histological analysis was performed and compared with MRI. RESULTS: In normal DVC, unlike conventional RARE-sequences, 3D-UTE allowed complete identification of DVC zonal anatomy including on visual analysis and CNR measurements. In pathological conditions, SNR and CNR measurements of the annulus fibrosus and nucleus pulposus on 3D-UTE distinguished early discitis at W1 from chronic discopathy (P < 0.001 for SNR and P < 0.001 for CNR). Neither the normal complete anatomy of the DVC nor its pathological patterns could be assessed on conventional sequences. CONCLUSIONS: Unlike conventional sequences, 3D-UTE enables visualization of the complete normal DVC anatomy and enables monitoring of DDD differentiating between early DVC changes from chronic ones. LEVEL OF EVIDENCE I: Diagnostic: individual cross-sectional studies with the consistently applied reference standard and blinding.

2D multislice MP2RAGE sequence for fast T1 mapping at 7 T: Application to mouse imaging and MR thermometry.

PURPOSE: To develop a 2D radial multislice MP2RAGE sequence for fast and reliable T1 mapping at 7 T in mice and for MR thermometry. METHODS: The 2D-MP2RAGE sequence was performed with the following parameters: TI1 -TI2 -MP2RAGETR = 1000-3000-9000 ms. The multiple dead times within the sequence were used for interleaved multislice acquisition, enabling one to acquire six slices in 9 seconds. The excitation pulse shape, inversion selectivity, and interslice gap were optimized. In vitro comparison with the inversion-recovery sequence was performed. The T1 variations with temperature were measured on tubes with T1 ranging from 800 ms to 2000 ms. The sequence was used to acquire T1 maps continuously during 30 minutes on the brain and abdomen of healthy mice. RESULTS: A three-lobe cardinal sine excitation pulse, combined with an inversion slice thickness and an interslice gap of respectively 150% and 50% of the imaging slice thickness, led to a SD and bias of the T1 measurements below 1% and 2%, respectively. A linear dependence of T1 with temperature was measured between 10°C and 60°C. In vivo, less than 1% variation was measured between successive T1 maps in the mouse brain. In the abdomen, no obvious in-plane motion artifacts were observed but respiratory motion in the slice dimension led to 6% T1 underestimation. CONCLUSION: The multislice MP2RAGE sequence could be used for fast whole-body T1 mapping and MR thermometry. Its reconstruction method would enable on-the-fly reconstruction.

Compressed-Sensing MP2RAGE sequence: Application to the detection of brain metastases in mice at 7T.

PURPOSE: To develop a Compressed Sensing (CS)-MP2RAGE sequence to drastically shorten acquisition duration and then detect and measure the T1 of brain metastases in mice at 7 T. METHODS: The encoding trajectory of the standard Cartesian MP2RAGE sequence has been modified (1) to obtain a variable density Poisson disk under-sampling distribution along the ky -kz plane, and (2) to sample the central part of the k-space exactly at TI1 and TI2 inversion times. In a prospective study, the accuracy of the T1 measurements was evaluated on phantoms containing increasing concentrations of gadolinium. The CS acceleration factors were increased to evaluate their influence on the contrast and T1 measurements of brain metastases in vivo. Finally, the 3D T1 maps were acquired with at 4-fold increased spatial resolution. The volumes and T1 values of the metastases were measured while using CS to reduce scan time. RESULTS: The implementation of the CS-encoding trajectory did not affect the T1 measurements in vitro. Accelerating the acquisition by a factor of 2 did not alter the contrast or the T1 values of the brain metastases. 3D T1 maps could be obtained in < 1 min using a CS factor of 6. Increasing the spatial resolution enabled more accurately measurement of the metastasis volumes while maintaining an acquisition duration below 5 min. CONCLUSION: The CS-MP2RAGE sequence could be of great interest in oncology to either rapidly obtain mouse brain 3D T1 maps or to increase the spatial resolution with no penalty on the scan duration.

Radial MP2RAGE sequence for rapid 3D T1 mapping of mouse abdomen: application to hepatic metastases.

OBJECTIVES: The T1 longitudinal recovery time is regarded as a biomarker of cancer treatment efficiency. In this scope, the Magnetization Prepared 2 RApid Gradient Echo (MP2RAGE) sequence relevantly complies with fast 3D T1 mapping. Nevertheless, with its Cartesian encoding scheme, it is very sensitive to respiratory motion. Consequently, a radial encoding scheme was implemented for the detection and T1 measurement of hepatic metastases in mice at 7T. METHODS: A 3D radial encoding scheme was developed using a golden angle distribution for the k-space trajectories. As in that case, each projection contributes to the image contrast, the signal equations had to be modified. Phantoms containing increasing gadoteridol concentrations were used to determine the accuracy of the sequence in vitro. Healthy mice were repetitively scanned to assess the reproducibility of the T1 values. The growth of hepatic metastases was monitored. Undersampling robustness was also evaluated. RESULTS: The accuracy of the T1 values obtained with the radial MP2RAGE sequence was > 90% compared to the Inversion-Recovery sequence. The motion robustness of this new sequence also enabled repeatable T1 measurements on abdominal organs. Hepatic metastases of less than 1-mm diameter were easily detected and T1 heterogeneities within the metastasis and between the metastases within the same animal were measured. With a twofold acceleration factor using undersampling, high-quality 3D T1 abdominal maps were achieved in 9 min. CONCLUSIONS: The radial MP2RAGE sequence could be used for fast 3D T1 mapping, to detect and characterize metastases in regions subjected to respiratory motion. KEY POINTS: • The Cartesian encoding of the MP2RAGE sequence was modified to a radial encoding. The modified sequence enabled accurate T 1 measurements on phantoms and on abdominal organs of mice. • Hepatic metastases were easily detected due to high contrast. Heterogeneity in T 1 was measured within the metastases and between each metastasis within the same animal. • As implementation of this sequence does not require specific hardware, we expect that it could be readily available for clinical practice in humans.

Fast 3D ultrashort echo-time spiral projection imaging using golden-angle: A flexible protocol for in vivo mouse imaging at high magnetic field.

PURPOSE: To develop a fast three-dimensional (3D) k-space encoding method based on spiral projection imaging (SPI) with an interleaved golden-angle approach and to validate this novel sequence on small animal models. METHODS: A disk-like trajectory, in which each disk contained spirals, was developed. The 3D encoding was performed by tilting the disks with a golden angle. The sharpness was first calculated at different T2* values. Then, the sharpness was measured on phantom using variable undersampling ratios. Finally, the sampling method was validated by whole brain time-of-flight angiography and ultrasmall superparamagnetic iron oxide (USPIO) enhanced free-breathing liver angiography on mouse. RESULTS: The in vitro results demonstrated the robustness of the method for short T2* and high undersampling ratios. In vivo experiments showed the ability to properly detect small vessels in the brain with an acquisition time shorter than 1 min. Free-breathing mice liver angiography showed the insensitivity of this protocol toward motions and flow artifacts, and enabled the visualization of liver motion during breathing. CONCLUSIONS: The method implemented here allowed fast 3D k-space sampling with a high undersampling ratio. Combining the advantages of center-out spirals with the flexibility of the golden angle approach could have major implications for real-time imaging. Magn Reson Med 77:1831-1840, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

USPIO-enhanced 3D-cine self-gated cardiac MRI based on a stack-of-stars golden angle short echo time sequence: Application on mice with acute myocardial infarction.

PURPOSE: To develop and assess a 3D-cine self-gated method for cardiac imaging of murine models. MATERIALS AND METHODS: A 3D stack-of-stars (SOS) short echo time (STE) sequence with a navigator echo was performed at 7T on healthy mice (n = 4) and mice with acute myocardial infarction (MI) (n = 4) injected with ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles. In all, 402 spokes were acquired per stack with the incremental or the golden angle method using an angle increment of (360/402)° or 222.48°, respectively. A cylindrical k-space was filled and repeated with a maximum number of repetitions (NR) of 10. 3D cine cardiac images at 156 µm resolution were reconstructed retrospectively and compared for the two methods in terms of contrast-to-noise ratio (CNR). The golden angle images were also reconstructed with NR = 10, 6, and 3, to assess cardiac functional parameters (ejection fraction, EF) on both animal models. RESULTS: The combination of 3D SOS-STE and USPIO injection allowed us to optimize the identification of cardiac peaks on navigator signal and generate high CNR between blood and myocardium (15.3 ± 1.0). The golden angle method resulted in a more homogeneous distribution of the spokes inside a stack (P < 0.05), enabling reducing the acquisition time to 15 minutes. EF was significantly different between healthy and MI mice (P < 0.05). CONCLUSION: The method proposed here showed that 3D-cine images could be obtained without electrocardiogram or respiratory gating in mice. It allows precise measurement of cardiac functional parameters even on MI mice. J. Magn. Reson. Imaging 2016;44:355-365.

Computational Modelling of Metastasis Development in Renal Cell Carcinoma.

The biology of the metastatic colonization process remains a poorly understood phenomenon. To improve our knowledge of its dynamics, we conducted a modelling study based on multi-modal data from an orthotopic murine experimental system of metastatic renal cell carcinoma. The standard theory of metastatic colonization usually assumes that secondary tumours, once established at a distant site, grow independently from each other and from the primary tumour. Using a mathematical model that translates this assumption into equations, we challenged this theory against our data that included: 1) dynamics of primary tumour cells in the kidney and metastatic cells in the lungs, retrieved by green fluorescent protein tracking, and 2) magnetic resonance images (MRI) informing on the number and size of macroscopic lesions. Critically, when calibrated on the growth of the primary tumour and total metastatic burden, the predicted theoretical size distributions were not in agreement with the MRI observations. Moreover, tumour expansion only based on proliferation was not able to explain the volume increase of the metastatic lesions. These findings strongly suggested rejection of the standard theory, demonstrating that the time development of the size distribution of metastases could not be explained by independent growth of metastatic foci. This led us to investigate the effect of spatial interactions between merging metastatic tumours on the dynamics of the global metastatic burden. We derived a mathematical model of spatial tumour growth, confronted it with experimental data of single metastatic tumour growth, and used it to provide insights on the dynamics of multiple tumours growing in close vicinity. Together, our results have implications for theories of the metastatic process and suggest that global dynamics of metastasis development is dependent on spatial interactions between metastatic lesions.

Time-resolved TOF MR angiography in mice using a prospective 3D radial double golden angle approach.

PURPOSE: To develop an undersampled anatomical, three-dimensional (3-D) time-resolved magnetic resonance angiography (MRA) method for small animals based on time-of-flight (TOF) effect and radial sampling. METHODS: Mouse carotid arteries and Circle of Willis images were acquired on a 7T scanner with an electrocardiogram (ECG)-triggered sequence. Preliminary experiments were used to generate an approximately uniform distribution of radial projections with a first golden angle and to produce anatomical TOF images. A second golden angle ratio between consecutive projections of cine acquisitions was added to make it possible to use a temporal filter during reconstruction of time-resolved angiography. A decreasing number of projections were tested, and their impact on signal-to-noise ratio (SNR) and spatial resolution was assessed. RESULTS: In anatomical MRA, the undersampled radial approach efficiently allows fast acquisition of mouse angiogram in 3D (22 sec). It was also only slightly sensitive to motion and flow artifacts. The time-resolved sequence can be performed with only 2,500 projections per cine and a temporal resolution under 4 ms in a relatively short acquisition time (less than 5 min). CONCLUSION: This technique simultaneously provided high 3D isotropic spatial resolution and excellent temporal resolution with a good SNR level, allowing blood flow to be visualized in a restricted acquisition time.

Fast and robust 3D T1 mapping using spiral encoding and steady RF excitation at 7 T: application to cardiac manganese enhanced MRI (MEMRI) in mice.

Mapping longitudinal relaxation times in 3D is a promising quantitative and non-invasive imaging tool to assess cardiac remodeling. Few methods are proposed in the literature allowing us to perform 3D T1 mapping. These methods often require long scan times and use a low number of 3D images to calculate T1 . In this project, a fast 3D T1 mapping method using a stack-of-spirals sampling scheme and regular RF pulse excitation at 7 T is presented. This sequence, combined with a newly developed fitting procedure, allowed us to quantify T1 of the whole mouse heart with a high spatial resolution of 208 × 208 × 315 µm(3) in 10-12 min acquisition time. The sensitivity of this method for measuring T1 variations was demonstrated on mouse hearts after several injections of manganese chloride (doses from 25 to 150 µmol kg(-1) ). T1 values were measured in vivo in both pre- and post-contrast experiments. This protocol was also validated on ischemic mice to demonstrate its efficiency to visualize tissue damage induced by a myocardial infarction. This study showed that combining spiral gradient shape and steady RF excitation enabled fast and robust 3D T1 mapping of the entire heart with a high spatial resolution.

Orotracheal administration of contrast agents: a new protocol for brain tumor targeting.

The development of new non-invasive diagnostic and therapeutic approaches is of paramount importance in order to improve the outcome of patients with glioblastoma (GBM). In this work we investigated a completely non-invasive pre-clinical protocol to effectively target and detect brain tumors through the orotracheal route, using ultra-small nanoparticles (USRPs) and MRI. A mouse model of GBM was developed. In vivo MRI acquisitions were performed before and after intravenous or orotracheal administration of the nanoparticles to identify and segment the tumor. The accumulation of the nanoparticles in neoplastic lesions was assessed ex vivo through fluorescence microscopy. Before the administration of contrast agents, MR images allowed the identification of the presence of abnormal brain tissue in 73% of animals. After orotracheal or intravenous administration of USRPs, in all the mice an excellent co-localization of the position of the tumor with MRI and histology was observed. The elimination time of the USRPs from the tumor after the orotracheal administration was approximately 70% longer compared with intravenous injection. MRI and USRPs were shown to be powerful imaging tools able to detect, quantify and longitudinally monitor the development of GBMs. The absence of ionizing radiation and high resolution of MRI, along with the complete non-invasiveness and good reproducibility of the proposed protocol, make this technique potentially translatable to humans. To our knowledge, this is the first time that the advantages of a needle-free orotracheal administration route have been demonstrated for the investigation of the pathomorphological changes due to GBMs.

Self-gated bSSFP sequences to detect iron-labeled cancer cells and/or metastases in vivo in mouse liver at 7 Tesla.

BACKGROUND: To develop and evaluate three-dimensional (3D) self-gated balanced steady state free precession (bSSFP) imaging at high magnetic fields to track iron-labeled cells and metastases in murine abdomens. METHODS: Mice were injected intravenously with iron-labeled melanoma cells and imaged at 7 Tesla (T). Respiration peaks were identified using Free Induction Decay acquired immediately after the radiofrequency pulse. Respiration-corrupted k-space lines were deleted. Four images were acquired to reconstruct final images using the Sum-Of-Square technique. Image sharpness, metastasis contrast and iron-labeled cell detection with SG-bSSFP sequence (acquired with echo time [TE] = 3 ms or TE = 6 ms) were compared with standard methods (gradient echo (GRE) and RARE). RESULTS: After reconstruction, the 3D SG-bSSFP images were 75-80% sharper, free from banding (75% liver signal-to-noise ratio recovery) and respiratory motion (26-42% improvement in signal homogeneity) artifacts. Metastasis contrast was twice higher on SG-bSSFP with TE = 3 ms than on RARE images. Iron-labeled cells and metastases were simultaneously detected on SG-bSSFP images with TE = 6 ms, with similar void intensity and tumor contrast to GRE and RARE, respectively. Halving acquisition time preserved iron sensitivity and metastasis contrast, allowing for 3D abdomen imaging in 13 min (TE = 3 ms) or 26 min (TE = 6 ms). CONCLUSION: Combining a self-gating technique with bSSFP sequences at 7T provides high-resolution 3D artifact-free abdominal images of small animals.

Longitudinal anatomical and metabolic MRI characterization of orthotopic xenograft prostate tumors in nude mice.

PURPOSE: To assess anatomic and functional magnetic resonance imaging (MRI) for monitoring of tumor volume and metabolism of orthotopic xenograft prostate cancer tumors. MATERIALS AND METHODS: Human-derived PC-3M cells were implanted into the prostate in 22 nude mice. Tumor volume and MRI appearance were monitored for up to 29 days. Histology was performed to detect metastases. Hyperpolarized [1-(13) C]pyruvate MRI was used to measure tumor metabolism on day 22. RESULTS: Tumors were visible by MRI 9 days after tumor cell implantation. Tumor volume increased to 720 ± 190 mm(3) on day 29 of imaging. Metastasis was seen in the iliac lymph nodes at all timepoints, and in more distant lymph nodes at later timepoints, but was not detectable by MRI. Regions with low pyruvate uptake corresponded to regions with necrosis and had a higher lactate/pyruvate ratio (0.98 ± 0.4 vs. 1.6 ± 1.1). CONCLUSION: MRI using the balanced steady-state free precession (bSSFP) sequence can be used to monitor tumor growth in orthotopic PC-3M tumors as early as 9 days post-injection. Hyperpolarized pyruvate MRI has potential to assess tumor metabolism and necrosis.

Extensive expansion of primary human gamma delta T cells generates cytotoxic effector memory cells that can be labeled with Feraheme for cellular MRI.

Gamma delta T cells (GDTc) comprise a small subset of cytolytic T cells shown to kill malignant cells in vitro and in vivo. We have developed a novel protocol to expand GDTc from human blood whereby GDTc were initially expanded in the presence of alpha beta T cells (ABTc) that were then depleted prior to use. We achieved clinically relevant expansions of up to 18,485-fold total GDTc, with 18,849-fold expansion of the Vδ1 GDTc subset over 21 days. ABTc depletion yielded 88.1 ± 4.2 % GDTc purity, and GDTc continued to expand after separation. Immunophenotyping revealed that expanded GDTc were mostly CD27-CD45RA- and CD27-CD45RA+ effector memory cells. GDTc cytotoxicity against PC-3M prostate cancer, U87 glioblastoma and EM-2 leukemia cells was confirmed. Both expanded Vδ1 and Vδ2 GDTc were cytotoxic to PC-3M in a T cell antigen receptor- and CD18-dependent manner. We are the first to label GDTc with ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles for cellular MRI. Using protamine sulfate and magnetofection, we achieved up to 40 % labeling with clinically approved Feraheme (Ferumoxytol), as determined by enumeration of Perls' Prussian blue-stained cytospins. Electron microscopy at 2,800× magnification verified the presence of internalized clusters of iron oxide; however, high iron uptake correlated negatively with cell viability. We found improved USPIO uptake later in culture. MRI of GDTc in agarose phantoms was performed at 3 Tesla. The signal-to-noise ratios for unlabeled and labeled cells were 56 and 21, respectively. Thus, Feraheme-labeled GDTc could be readily detected in vitro via MRI.

The Compressed Sensing MP2RAGE as a Surrogate to the MPRAGE for Neuroimaging at 3 T.

OBJECTIVES: The magnetization-prepared 2 rapid acquisition gradient echo (MP2RAGE) sequence provides quantitative T1 maps in addition to high-contrast morphological images. Advanced acceleration techniques such as compressed sensing (CS) allow its acquisition time to be compatible with clinical applications. To consider its routine use in future neuroimaging protocols, the repeatability of the segmented brain structures was evaluated and compared with the standard morphological sequence (magnetization-prepared rapid gradient echo [MPRAGE]). The repeatability of the T1 measurements was also assessed. MATERIALS AND METHODS: Thirteen healthy volunteers were scanned either 3 or 4 times at several days of interval, on a 3 T clinical scanner, with the 2 sequences (CS-MP2RAGE and MPRAGE), set with the same spatial resolution (0.8-mm isotropic) and scan duration (6 minutes 21 seconds). The reconstruction time of the CS-MP2RAGE outputs (including the 2 echo images, the MP2RAGE image, and the T1 map) was 3 minutes 33 seconds, using an open-source in-house algorithm implemented in the Gadgetron framework.Both precision and variability of volume measurements obtained from CAT12 and VolBrain were assessed. The T1 accuracy and repeatability were measured on phantoms and on humans and were compared with literature.Volumes obtained from the CS-MP2RAGE and the MPRAGE images were compared using Student t tests (P < 0.05 was considered significant). RESULTS: The CS-MP2RAGE acquisition provided morphological images of the same quality and higher contrasts than the standard MPRAGE images. Similar intravolunteer variabilities were obtained with the CS-MP2RAGE and the MPRAGE segmentations. In addition, high-resolution T1 maps were obtained from the CS-MP2RAGE. T1 times of white and gray matters and several deep gray nuclei are consistent with the literature and show very low variability (<1%). CONCLUSIONS: The CS-MP2RAGE can be used in future protocols to rapidly obtain morphological images and quantitative T1 maps in 3-dimensions while maintaining high repeatability in volumetry and relaxation times.

Deep learning model for automatic segmentation of lungs and pulmonary metastasis in small animal MR images.

Lungs are the most frequent site of metastases growth. The amount and size of pulmonary metastases acquired from MRI imaging data are the important criteria to assess the efficacy of new drugs in preclinical models. While efficient solutions both for MR imaging and the downstream automatic segmentation have been proposed for human patients, both MRI lung imaging and segmentation in preclinical animal models remains challenging due to the physiological motion (respiratory and cardiac movements), to the low amount of protons in this organ and to the particular challenge of precise segmentation of metastases. As a consequence post-mortem analysis is currently required to obtain information on metastatic volume. In this work, we have developed a complete methodological pipeline for automated analysis of lungs and metastases in mice, consisting of an MR sequence for image acquisition and a deep learning method for automatic segmentation of both lungs and metastases. On one hand, we optimized an MR sequence for mouse lung imaging with high contrast for high detection sensitivity. On the other hand we developed DeepMeta, a multiclass U-Net 3+ deep learning model to automatically segment the images. To assess if the proposed deep learning pipeline is able to provide an accurate segmentation of both lungs and pulmonary metastases, we have longitudinally imaged mice with fast- and slow-growing metastasis. Fifty-five balb/c mice were injected with two different derivatives of renal carcinoma cells. Mice were imaged with a SG-bSSFP (self-gated balanced steady state free precession) sequence at different time points after the injection of cancer cells. Both lung and metastases segmentations were manually performed by experts. DeepMeta was trained to perform lung and metastases segmentation based on the resulting ground truth annotations. Volumes of lungs and of pulmonary metastases as well as the number of metastases per mouse were measured on a separate test dataset of MR images. Thanks to the SG method, the 3D bSSFP images of lungs were artifact-free, enabling the downstream detection and serial follow-up of metastases. Moreover, both lungs and metastases segmentation was accurately performed by DeepMeta as soon as they reached the volume of ∼ 0.02 m m 3 . Thus we were able to distinguish two groups of mice in terms of number and volume of pulmonary metastases as well as in terms of the slow versus fast patterns of growth of metastases. We have shown that our methodology combining SG-bSSFP with deep learning, enables processing of the whole animal lungs and is thus a viable alternative to histology alone.

In vivo MR tracking of therapeutic microglia to a human glioma model.

A knowledge of the spatial localization of cell vehicles used in gene therapy against glioma is necessary before launching therapy. For this purpose, MRI cell tracking is performed by labeling the cell vehicles with contrast agents. In this context, the goal of this study was to follow noninvasively the chemoattraction of therapeutic microglial cells to a human glioma model before triggering therapy. Silica nanoparticles grafted with gadolinium were used to label microglia. These vehicles, expressing constitutively the thymidine kinase suicide gene fused to the green fluorescent protein gene, were injected intravenously into human glioma-bearing nude mice. MRI was performed at 4.7 T to track noninvasively microglial accumulation in the tumor. This was followed by microscopy on brain slices to assess the presence in the glioma of the contrast agents, microglia and fusion gene through the detection of silica nanoparticles grafted with tetramethyl rhodamine iso-thiocyanate, 3,3'-dioctadecyloxacarbocyanine perchlorate and green fluorescent protein fluorescence, respectively. Finally, gancyclovir was administered systemically to mice. Human microglia were detectable in living mice, with strong negative contrast on T(2) *-weighted MR images, at the periphery of the glioma only 24 h after systemic injection. The location of the dark dots was identical in MR microscopy images of the extracted brains at 9.4 T. Fluorescence microscopy confirmed the presence of the contrast agents, exogenous microglia and suicide gene in the intracranial tumor. In addition, gancyclovir treatment allowed an increase in mice survival time. This study validates the MR tracking of microglia to a glioma after systemic injection and their use in a therapeutic strategy against glioma.

In vivo single scan detection of both iron-labeled cells and breast cancer metastases in the mouse brain using balanced steady-state free precession imaging at 1.5 T.

PURPOSE: To simultaneously detect iron-labeled cancer cells and brain tumors in vivo in one scan, the balanced steady-state free precession (b-SSFP) imaging sequence was optimized at 1.5 T on mice developing brain metastases subsequent to the injection of micron-sized iron oxide particle-labeled human breast cancer cells. MATERIALS AND METHODS: b-SSFP sequence parameters (repetition time, flip angle, and receiver bandwidth) were varied and the signal-to-noise ratio, contrast between the brain and tumors, and the number of detected iron-labeled cells were evaluated. RESULTS: Optimal b-SSFP images were acquired with a 26 msec repetition time, 35° flip angle, and bandwidth of ±21 kHz. b-SSFP images were compared with T(2) -weighted 2D fast spin echo (FSE) and 3D spoiled gradient recalled echo (SPGR) images. The mean tumor-brain contrast-to-noise ratio and the ability to detect iron-labeled cells were the highest in the b-SSFP images. CONCLUSION: A single b-SSFP scan can be used to visualize both iron-labeled cells and brain metastases.

Micron-sized iron oxide particles for both MRI cell tracking and magnetic fluid hyperthermia treatment.

Iron oxide particles (IOP) are commonly used for Cellular Magnetic Resonance Imaging (MRI) and in combination with several treatments, like Magnetic Fluid Hyperthermia (MFH), due to the rise in temperature they provoke under an Alternating Magnetic Field (AMF). Micrometric IOP have a high sensitivity of detection. Nevertheless, little is known about their internalization processes or their potential heat power. Two micrometric commercial IOP (from Bangs Laboratories and Chemicell) were characterized by Transmission Electron Microscopy (TEM) and their endocytic pathways into glioma cells were analyzed. Their Specific Absorption Rate (SAR) and cytotoxicity were evaluated using a commercial AMF inductor. T2-weighted imaging was used to monitor tumor growth in vivo after MFH treatment in mice. The two micron-sized IOP had similar structures and r2 relaxivities (100 mM-1 s-1) but involved different endocytic pathways. Only ScreenMAG particles generated a significant rise in temperature following AMF (SAR = 113 W g-1 Fe). After 1 h of AMF exposure, 60% of ScreenMAG-labeled cells died. Translated to a glioma model, 89% of mice responded to the treatment with smaller tumor volume 42 days post-implantation. Micrometric particles were investigated from their characterization to their intracellular internalization pathways and applied in one in vivo cancer treatment, i.e. MFH.