Browsing by Author "Johnson, G Allan"

Mice have become the preferred model system for studying brain function and disease. With the powerful genetic tools available, mouse models can be created to study the underlying molecular basis of neurobiology in vivo. Just as magnetic resonance imaging is the dominant tool for evaluating the human brain, high-resolution MRI--magnetic resonance microscopy (MRM)--is a useful tool for studying the brain of mouse models. However, the need for high spatial resolution limits the signal-to-noise ratio (SNR) of the MRM images. To address this problem, T1-shortening contrast agents can be used, which not only improve the tissue contrast-to-noise ratio (CNR) but also increase SNR by allowing the MR signal to recover faster between pulses. By "actively staining" the tissue with these T1-shortening agents, MRM can be performed with higher resolution, greater contrast, and shorter scan times. In this work, active staining with T1-shortening agents was used to enhance three types of in vivo mouse brain MRM: (1) angiographic imaging of the neurovasculature, (2) anatomical imaging of the brain parenchyma, and (3) functional imaging of neuronal activity.

For magnetic resonance angiography (MRA) of the mouse, typical contrast agents are not useful because they are quickly cleared by the body and/or extravasate from the blood pool before a high-resolution image can be acquired. To address these limitations, a novel contrast agent--SC-Gd liposomes--has been developed, which is cleared slowly by the body and is too large to extravasate from the blood pool. In this work, MRA protocols were optimized for both the standard technique (time-of-flight contrast) and SC-Gd liposomes. When the blood was stained with SC-Gd liposomes, small vessel CNR improved to 250% that of time-of-flight. The SC-Gd liposomes could also be used to reduce scan time by 75% while still improving CNR by 32%.

For MRM of the mouse brain parenchyma, active staining has been used to make dramatic improvements in the imaging of ex vivo specimens. However for in vivo imaging, the blood-brain barrier (BBB) prevents T1-shortening agents from entering the brain parenchyma. In this work, a noninvasive technique was developed for BBB opening with microbubbles and ultrasound (BOMUS). Using BOMUS, the parenchyma of the brain could be actively stained with the T1-shortening contrast agent, Gd-DTPA, and MRM images could be acquired in vivo with unprecedented resolution (52 x 52 x 100 micrometers3) in less than 1 hour.

Functional MRI (fMRI), which uses blood oxygen level dependant (BOLD) contrast to detect neuronal activity, has been a revolutionary technique for studying brain function in humans. However, in mice, BOLD contrast has been difficult to detect and thus routine fMRI in mice has not been feasible. An alternative approach for detecting neuronal activity uses manganese (Mn2+). Mn2+ is a T1-shortening agent that can enter depolarized neurons via calcium channels. Thus, Mn2+ is a functional contrast agent with affinity for active neurons. In this work, Mn2+ (administered with the BOMUS technique) was used to map the neuronal response to stimulation of the vibrissae. The resultant activation map showed close agreement to published maps of the posterior-lateral and anterior-medial barrel field of the primary sensory cortex.

The use of T1-shortening agents to actively stain tissues of interest--blood, brain parenchyma, or active neurons--will facilitate the use of MRM for studying mouse models of brain development, function, and disease.

Understanding the structure of the brain has been a major goal of neuroscience research over the past century, driven in part by the understanding that brain structure closely follows function. Normative brain maps, or atlases, can be used to understand normal brain structure, and to identify structural differences resulting from disease. Recently, diffusion tensor magnetic resonance imaging has emerged as a powerful tool for brain atlasing; however, its utility is hindered by image resolution and signal limitations. These limitations can be overcome by imaging fixed ex-vivo specimens stained with MRI contrast agents, a technique known as diffusion tensor magnetic resonance histology (DT-MRH). DT-MRH represents a unique, quantitative tool for mapping the brain with unprecedented structural detail. This technique has engendered a new generation of 3D, digital brain atlases, capable of representing complex dynamic processes such as neurodevelopment. This dissertation explores the use of DT-MRH for quantitative brain atlasing in an animal model and initial work in the human brain.

Chapter 1 describes the advantages of the DT-MRH technique, and the motivations for generating a quantitative atlas of rat postnatal neurodevelopment. The second chapter covers optimization of the DT-MRH hardware and pulse sequence design for imaging the developing rat brain. Chapter 3 details the acquisition and curation of rat neurodevelopmental atlas data. Chapter 4 describes the creation and implementation of an ontology-based segmentation scheme for tracking changes in the developing brain. Chapters 5 and 6 pertain to analyses of volumetric changes and diffusion tensor parameter changes throughout rat postnatal neurodevelopment, respectively. Together, the first six chapters demonstrate many of the unique and scientifically valuable features of DT-MRH brain atlases in a popular animal model.

The final two chapters are concerned with translating the DT-MRH technique for use in human and non-human primate brain atlasing. Chapter 7 explores the validity of assumptions imposed by DT-MRH in the primate brain. Specifically, it analyzes computer models and experimental data to determine the extent to which intravoxel diffusion complexity exists in the rhesus macaque brain, a close model for the human brain. Finally, Chapter 8 presents conclusions and future directions for DT-MRH brain atlasing, and includes initial work in creating DT-MRH atlases of the human brain. In conclusion, this work demonstrates the utility of a DT-MRH brain atlasing with an atlas of rat postnatal neurodevelopment, and lays the foundation for creating a DT-MRH atlas of the human brain.

Dynamic contrast-enhanced (DCE) MRI has been widely used as a quantitative imaging method for monitoring tumor response to therapy. The pharmacokinetic parameters derived from this technique have been used in more than 100 phase I trials and investigator led studies. The simultaneous challenges of increasing the temporal and spatial resolution, in a setting where the signal from the much smaller voxel is weaker, have made this MR technique difficult to implement in small-animal imaging. Existing preclinical DCE-MRI protocols acquire a limited number of slices resulting in potentially lost information in the third dimension. Furthermore, drug efficacy studies measuring the effect of an anti-angiogenic treatment, often compare the derived biomarkers on manually selected tumor regions or over the entire volume. These measurements include domains where the interpretation of the biomarkers may be unclear (such as in necrotic areas).

This dissertation describes and compares a family of four-dimensional (3D spatial + time), projection acquisition, keyhole-sampling strategies that support high spatial and temporal resolution. An interleaved 3D radial trajectory with a quasi-uniform distribution of points in k-space was used for sampling temporally resolved datasets. These volumes were reconstructed with three different k-space filters encompassing a range of possible keyhole strategies. The effect of k-space filtering on spatial and temporal resolution was studied in phantoms and in vivo. The statistical variation of the DCE-MRI measurement is analyzed by considering the fundamental sources of error in the MR signal intensity acquired with the spoiled gradient-echo (SPGR) pulse sequence. Finally, the technique was applied for measuring the extent of the opening of the blood-brain barrier in a mouse model of pediatric glioma and for identifying regions of therapeutic effect in a model of colorectal adenocarcinoma.

It is shown that 4D radial keyhole imaging does not degrade the system spatial and temporal resolution at a cost of 20-40% decrease in SNR. The time-dependent concentration of the contrast agent measured in vivo is within the theoretically predicted limits. The uncertainty in measuring the pharmacokinetic parameters with the sequences is of the same order, but always higher than, the uncertainty in measuring the pre-injection longitudinal relaxation time. The histogram of the time-to-peak provides useful knowledge about the spatial distribution of K^trans and microvascular density. Two regions with distinct kinetic parameters were identified when the TTP map from DCE-MRM was thresholded at 1000 sec. The effect of bevacizumab, as measured by a decrease in K^trans, was confined to one of these regions. DCE-MRI studies may contribute unique insights into the response of the tumor microenvironment to therapy.

Research using mice and rats has gained interest because they are robust test beds for clinical drug development and are used to elucidate disease etiologies. Blood vessel visualization and blood flow measurements are important anatomic and physiologic indicators to drug/disease stimuli or genetic modification. Cardio-pulmonary blood flow is an important indicator of heart and lung performance. Small animal functional imaging provides a way to measure physiologic changes minimally-invasively while the animal is alive, thereby allowing for multiple measurements in the same animal with little physiologic perturbation. Current methods of measuring cardio-pulmonary blood flow suffer from some or all of these limitations-they produce relative measurements, are limited to global or whole animal or organ regions, do not provide vasculature visualization, limited to a few or singular samples per animal, are not able to measure acute changes, or are very invasive or requires animal sacrifice. The focus of this work was the development of a small animal x-ray imaging system capable of minimally invasive real-time, high resolution vascular visualization, and cardio-pulmonary blood flow measurements in the live animal. The x-ray technique used was digital subtraction angiography (DSA). This technique is a particularly appealing approach because it is easy to use, can capture rapid physiological changes on a heart beat-to-beat basis, and provides anatomical and functional vasculature information. This DSA system is special because it was designed and implemented from the ground up to be optimized for small animal imaging and functional measurements. This system can perform: 1) minimally invasive in vivo blood flow measurements, 2) multiple measurements in the same animal in a rapid succession (every 30 seconds-a substantial improvement over singular measurements that require minutes to acquire by the Fick method), 3) very high resolution (up to 46 micron) vascular visualization, 4) quantitative blood flow measurements in absolute metrics (mL/min instead of arbitrary units or velocity) and relative blood volume dynamics from discrete ROIs, and 5) relative mean transit time dynamics on a pixel-by-pixel basis (100 µm x 100 µm). The end results are 1) anatomical vessel time course images showing the contrast agent flowing through the vasculature, 2) blood flow information of the live rat cardio-pulmonary system in absolute units and relative blood volume information at discrete ROIs of enhanced blood vessels, and 3) colormaps of relative transit time dynamics. This small animal optimized imaging system can be a useful tool in future studies to measure drug or disease modulated blood flow dynamics in the small animal.

The kidney's major role in filtration depends on its high blood flow, concentrating mechanisms, and biochemical activation. The kidney's greatest strengths also lead to vulnerability for drug-induced nephrotoxicity and other renal injuries. The current standard to diagnose renal injuries is with a percutaneous renal biopsy, which can be biased and insufficient. In one particular case, biopsy of a kidney with renal cell carcinoma can actually initiate metastasis. Tools that are sensitive and specific to detect renal disease early are essential, especially noninvasive diagnostic imaging. While other imaging modalities (ultrasound and x-ray/CT) have their unique advantages and disadvantages, MRI has superb soft tissue contrast without ionizing radiation. More importantly, there is a richness of contrast mechanisms in MRI that has yet to be explored and applied to study renal disease.

The focus of this work is to advance preclinical imaging tools to study the structure and function of the renal system. Studies were conducted in normal and disease models to understand general renal physiology as well as pathophysiology. This dissertation is separated into two parts--the first is the identification of renal architecture with ex vivo MRI; the second is the characterization of renal dynamics and function with in vivo MRI. High resolution ex vivo imaging provided several opportunities including: 1) identification of fine renal structures, 2) implementation of different contrast mechanisms with several pulse sequences and reconstruction methods, 3) development of image-processing tools to extract regions and structures, and 4) understanding of the nephron structures that create MR contrast and that are important for renal physiology. The ex vivo studies allowed for understanding and translation to in vivo studies. While the structure of this dissertation is organized by individual projects, the goal is singular: to develop magnetic resonance imaging biomarkers for renal system.

The work presented here includes three ex vivo studies and two in vivo studies:

1) Magnetic resonance histology of age-related nephropathy in sprague dawley.

2) Quantitative susceptibility mapping of kidney inflammation and fibrosis in type 1 angiotensin receptor-deficient mice.

3) Susceptibility tensor imaging of the kidney and its microstructural underpinnings.

4) 4D MRI of renal function in the developing mouse.

5) 4D MRI of polycystic kidneys in rapamycin treated Glis3-deficient mice.

Mouse models of cancer are an invaluable tool for studying the mechanism of the disease and the effect of new therapies. Recent years have seen an explosive growth in the development of such models and consequently there is an increased need for better imaging techniques to study them. The goal of this work was to develop a technique that satisfied the requirements for preclinical cancer imaging: high spatial resolution, good soft tissue differentiation, excellent motion immunity, fast and non-invasive imaging to enable high-throughput, longitudinal studies.

T₂-weighted and diffusion-weighted magnetic resonance imaging (MRI) has been shown to be effective for tumor characterization clinically. But translation of these techniques to the mouse is challenging. The higher spatial resolution and faster physiologic motion make conventional approaches very susceptible to phase artifacts. Additionally, at higher magnetic fields required for these studies, T*₂ and T₂ are significantly shorter and T₁ is longer, making in vivo imaging even harder.

A rigorous cancer imaging protocol was developed by optimizing and integrating various components of the system, including MR hardware, animal handling, and pulse sequence design to achieve reliable, repeatable and rapid imaging. The technique presented here relies heavily on the non-Cartesian sampling strategy of PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) MRI. The novel data acquisition and reconstruction overcomes the adverse effects of physiological motion, allows for rapid setup and acquisition and provides excellent tissue contrast. The sequence was optimized to enable T₂-weighted and diffusion-weighted imaging in tumor-bearing mice with in-plane resolution of 117μm and slice thickness of 1mm. Multi-slice datasets covering the entire thorax and abdomen were acquired in ∼30 minutes.

The imaging protocol developed here was applied to a high-throughput, longitudinal study in a mouse model of liver metastases. The liver is a common site of distal metastases in colon and rectal cancer, and if detected early has an improved prognosis. Unfortunately, severe respiratory motion make it hard to image. The relative merits of the proposed PROPELLER technique were analyzed with respect to the accepted gold-standard for abdominal cancer imaging, computed tomography (CT).

The non-Cartesian MR microscopy technique proposed here is a valuable tool in the “Cancer analysis toolkit”. It allows for high-throughput, longitudinal experiments in free-breathing mice generating both structural and functional information with minimal artifacts and excellent spatial resolution. This work should find broad applications in various mouse models of cancer for studying the pathology of the disease, its progression as well as its response to treatment.

In magnetic resonance microscopy, insufficient signal-to-noise ratio currently limits imaging performance. Superconducting probes can potentially increase the sensitivity of the magnetic resonance experiment. However, many superconducting probes failed to entirely deliver the expected increase in signal-to-noise ratio.

We present a method based on finite-element radiofrequency simulations. The radiofrequency model computes several figures of merit of a probe, namely: i) the resonant frequency, ii) the impedance, iii) the magnetic field homogeneity, iv) the filling factor, and v) the sensitivity. The probe is constituted by several components. The method calculates the electromagnetic losses induced by every component within the probe, and identifies the component limiting the sensitivity of the probe. Subsequently, the probe design can be improved iteratively.

We show that the sensitivity of an existing superconducting Helmholtz pair can be improved by increasing the filling factor of the probe and cooling the radiofrequency shield, which was implemented in the design of a new superconducting probe. The second probe exhibits a sensitivity three times as high, leading to improved imaging performance.