Compressed Sensing Accelerated Magnetic Resonance Spectroscopic Imaging

abstract: Magnetic resonance spectroscopic imaging (MRSI) is a valuable technique for assessing the in vivo spatial profiles of metabolites like N-acetylaspartate (NAA), creatine, choline, and lactate. Changes in metabolite concentrations can help identify tissue heterogeneity, providing prognostic and diagnostic information to the clinician. The increased uptake of glucose by solid tumors as compared to normal tissues and its conversion to lactate can be exploited for tumor diagnostics, anti-cancer therapy, and in the detection of metastasis. Lactate levels in cancer cells are suggestive of altered metabolism, tumor recurrence, and poor outcome. A dedicated technique like MRSI could contribute to an improved assessment of metabolic abnormalities in the clinical setting, and introduce the possibility of employing non-invasive lactate imaging as a powerful prognostic marker. However, the long acquisition time in MRSI is a deterrent to its inclusion in clinical protocols due to associated costs, patient discomfort (especially in pediatric patients under anesthesia), and higher susceptibility to motion artifacts. Acceleration strategies like compressed sensing (CS) permit faithful reconstructions even when the k-space is undersampled well below the Nyquist limit. CS is apt for MRSI as spectroscopic data are inherently sparse in multiple dimensions of space and frequency in an appropriate transform domain, for e.g. the wavelet domain. The objective of this research was three-fold: firstly on the preclinical front, to prospectively speed-up spectrally-edited MRSI using CS for rapid mapping of lactate and capture associated changes in response to therapy. Secondly, to retrospectively evaluate CS-MRSI in pediatric patients scanned for various brain-related concerns. Thirdly, to implement prospective CS-MRSI acquisitions on a clinical magnetic resonance imaging (MRI) scanner for fast spectroscopic imaging studies. Both phantom and in vivo results demonstrated a reduction in the scan time by up to 80%, with the accelerated CS-MRSI reconstructions maintaining high spectral fidelity and statistically insignificant errors as compared to the fully sampled reference dataset. Optimization of CS parameters involved identifying an optimal sampling mask for CS-MRSI at each acceleration factor. It is envisioned that time-efficient MRSI realized with optimized CS acceleration would facilitate the clinical acceptance of routine MRSI exams for a quantitative mapping of important biomarkers.Dissertation/ThesisDoctoral Dissertation Bioengineering 201

Intra- and Inter-Modality Registration for Validation of MRI based Hypoxia Imaging

abstract: Hypoxia is a pathophysiological condition which results from lack of oxygen supply in tumors. The assessment of tumor hypoxia and its response to therapies can provide guidelines for optimization and personalization of therapeutic protocols for better treatment. Previous research has shown the difficulty in measuring hypoxia anatomically due to its heterogenous nature. This makes the study of hypoxia through various imaging modalities and mapping techniques crucial. The potential of hypoxia targeting T1 contrast agent GdDO3NI in generating hypoxia maps has been studied earlier. In this work, the similarities between hypoxia maps generated by MRI using GdDO3NI and pimonidazole based immunohistochemistry (IHC) in non-small cell lung carcinoma bearing mice have been studied. Six NCI-H1975 tumor-bearing mice were studied. All animal studies were approved by Arizona State University’s Institute of Animal Care and Use Committee (IACUC). Post co-injection of GdDO3NI and pimonidazole, T1 weighted 3D gradient echo MR images were acquired. For ex-vivo analysis of hypoxia, 30 μm thick tumor sections were obtained for each harvested tumor and were stained for pimonidazole and counter-stained with DAPI for nuclear staining. Pimonidazole (PIMO) is clinically used as a “gold standard” hypoxia marker. The key process involved stacking and iterative registration based on quality metric SSIM (Structural Similarity) Index of DAPI stained images of 5 consecutive tumor sections to produce a 3D volume stack of 150 μm thickness. Information from the 3D volume is combined to produce one final slide by averaging. The same registration transform was applied to stack the pimonidazole images which were previously thresholded to highlight hypoxic regions. The registered IHC stack was then co-registered with a single thresholded T1 weighted gradient echo MRI slice of the same location (~156 μm thick) using an elastic B-splines transform. The same transform was applied to achieve the co-registration of pimonidazole and MR percentage enhancement image. Image similarity index after the co-registration was found to be greater than 0.5 for 5 of the animals suggesting good correlation. R2 values were calculated for both hypoxic regions as well as tumor boundaries. All the tumors showed a high boundary correlation value of R2 greater than 0.8. Half of the animals showed high R2 values greater than 0.5 for hypoxic fractions. The RMSE values for the co-registration of all the animals were found to be low further suggesting better correspondence and validating the MR based hypoxia imaging.Dissertation/ThesisMasters Thesis Biomedical Engineering 201

The extravascular penetration of tirapazamine into tumours: a predictive model of the transport and efficacy of hypoxia specific cytotoxic analogues and the potential use of cucurbiturils to facilitate delivery

A multiparameter model of the diffusion, antiproliferative assays IC 50 and aerobic and hypoxic clonogenic assays for a wide range of neutral and radical anion forms of tirapazamine (TPZ) analogues has found that: (a) extravascular diffusion is governed by the desolvation, lipophilicity, dipole moment and molecular volume, similar to passive and facilitated permeation through the blood brain barrier and other cellular membranes, (b) hypoxic assay properties of the TPZ analogues show dependencies on the electron affinity, as well as lipophilicity and dipole moment and desolvation, similar to other biological processes involving permeation of cellular membranes, including nuclear membranes, (c) aerobic properties are dependent on the almost exclusively on the electron affinity, consistent with electron transfer involving free radicals being dominant with little or no drug permeation of membranes, and most likely occurring in the extracellular matrix. Application of the model to the DNA binding equilibrium constants of TPZ analogues with acridine or acridine-like moieties show that ligand water desolvation and lipophilicity are the dominant processes governing the DNA intercalation of TPZ analogues. This conclusion is consistent with DFT modelling of the complexes formed by TPZ analogues with neutral and N-protonated acridine moieties which intercalate with the guanine DNA nucleobases. A quantum mechanical study has shown that TPZ can form stable complexes with cucurbit[7]uril as a precursor to proof of principle of improved TPZ delivery to tumours. Abbreviations Tirapazamine TPZ, free energy of water desolvation ΔG desolv,CDS , lipophilicity free energy ΔG lipo,CDS , cavity dispersion solvent structure of the first solvation shell CDS, multicellular layers MCL, extracellular matrix ECM, diffusion through support membrane D s , diffusion through multicellular layer D MCL , cucurbit[n]urils CB, cucurbit[7]urils, CB[7], highest occupied molecular orbital HOMO, lowest unoccupied molecular orbital LUMO, density functional molecular orbital theory DFT, adiabatic electron affinity AEA, cisplatin CisPt, ratio aerobic property:hypoxic property HCR, aerobic aer, hypoxic hyp, DNA binding equilibrium constant K DNA, multiple correlation coefficient R 2 , the F test of significance, standards errors for the estimate (SEE) and standard errors of the variables SE(ΔG desolCDS), SE(ΔG lipoCDS), SE(Dipole Moment), SE (Molecular Volume), SE(AEA)