A coarse-to-fine approach to prostate boundary segmentation in ultrasound images

BACKGROUND: In this paper a novel method for prostate segmentation in transrectal ultrasound images is presented. METHODS: A segmentation procedure consisting of four main stages is proposed. In the first stage, a locally adaptive contrast enhancement method is used to generate a well-contrasted image. In the second stage, this enhanced image is thresholded to extract an area containing the prostate (or large portions of it). Morphological operators are then applied to obtain a point inside of this area. Afterwards, a Kalman estimator is employed to distinguish the boundary from irrelevant parts (usually caused by shadow) and generate a coarsely segmented version of the prostate. In the third stage, dilation and erosion operators are applied to extract outer and inner boundaries from the coarsely estimated version. Consequently, fuzzy membership functions describing regional and gray-level information are employed to selectively enhance the contrast within the prostate region. In the last stage, the prostate boundary is extracted using strong edges obtained from selectively enhanced image and information from the vicinity of the coarse estimation. RESULTS: A total average similarity of 98.76%(± 0.68) with gold standards was achieved. CONCLUSION: The proposed approach represents a robust and accurate approach to prostate segmentation

Magnetite/silica core-shell nanoparticles for HER-2 targeted magnetic resonance imaging of breast tumours.

Contrast agents allow for greater detail of specific internal structures to be obtained under clinical MR imaging. These images are used to aid in the diagnosis of conditions or damage including tumours and other cancerous tissues. Gadolinium has for quite a while been used as a primary material for this purpose but increasing concerns regarding toxicity are adding pressure to seek alternate materials. Magnetite offers many properties that would make it an excellent contrast material and several products have come to market but are restricted in their application primarily due to particle size. This thesis aims to approach the problems associated with magnetite nanoparticles and their use in intravenous systems. This requires reducing the overall particle size and ensuring biocompatibility. This was accomplished by modifying the core particle size by altering the thermal decomposition parameters and surface coating the material with a layer of silica. A preliminary investigation was made using quasi cubic magnetite particles to investigate the biocompatibility and performance as an MR contrast agent. Based on these findings a second core shell nanoparticle system was formed using modified techniques to reduce the overall particle size by shrinking the core magnetite and the silica shell thickness. These particles were subsequently surface modified with Herceptin® to facilitate the selective uptake of the particles into specific cancerous 12 cells. The particles were examined for their biocompatibility, structural stability and selective uptake into SKBR3 cells in vitro and in vivo in live breast tumour baring mice. All the studies were undertaken in MRI scanners in use by clinicians at the Peter MacCallum Cancer Research Centre. This demonstrated that in a clinical setting, these core shell particles can be made to selectively target specific tumours in significant number to cause notable localised contrast at the target site

Cancer theranostics: multifunctional gold nanoparticles for diagnostics and therapy

Doctorate in Biology, Specialty in BiotechnologyThe use of gold nanoparticles (AuNPs) has been gaining momentum in molecular diagnostics due to their unique physico-chemical properties these systems present huge advantages, such as increased sensitivity, reduced cost and potential for single-molecule characterisation. Because of their versatility and easy of functionalisation, multifunctional AuNPs have also been proposed as optimal delivery systems for therapy (nanovectors). Being able to produce such systems would mean the dawn of a new age in theranostics (diagnostics and therapy)driven by nanotechnology vehicles. Nanotechnology can be exploit for cancer theranostics via the development of diagnostics systems such as colorimetric and imunoassays, and in therapy approaches through gene therapy, drug delivery and tumour targeting systems. The unique characteristics of nanoparticles in the nanometre range, such as high surface-tovolume ratio or shape/size-dependent optical properties, are drastically different from those of their bulk materials and hold pledge in the clinical field for disease therapeutics This PhD project intends to optimise a gold-nanoparticle based technique for the detection of oncogenes’ transcripts (c-Myc and BCR-ABL) that can be used for the evaluation of the expression profile in cancer cells, while simultaneously developing an innovative platform of multifunctional gold nanoparticles (tumour markers, cell penetrating peptides, fluorescent dyes) loaded with siRNA capable of silencing the selected proto-oncogenes, which can be used to evaluate the level of expression and determine the efficiency of silencing. This work is a part of an ongoing collaboration between Research Centre for Human Molecular Genetics, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Portugal and Biofunctional Nanoparticles and Surfaces Group, Instituto de Nanociencia de Aragón, Spain within a European project [NanoScieE+ - NANOTRUCK]. In order to achieve this goal we developed effective conjugation strategies to combine, in a highly controlled way, biomolecules to the surface of AuNPs with specific functions such as: ssDNA oligos to detect specific sequences and for mRNA quantification; Biofunctional spacers: Poly(ethylene glycol) (PEG) spacers used to increase solubility and biocompatibility and confer chemical functionality; Cell penetrating peptides: to overcome the lipophilic barrier of the cellular membranes and deliver molecules into cells using TAT peptide to achieve cytoplasm and nucleus; Quaternary ammonium: to introduce stable positively charged in gold nanoparticles surface; and RNA interference: siRNA complementary to a master regulator gene, the proto-oncogene c-Myc, that is implicated in cell growth, proliferation, loss of differentiation, and cell death. In order to establish that they are viable alternatives to the available methods, these innovative nanoparticles were extensively characterized on their chemical functionalization, ease of uptake, cellular toxicity and inflammation, and knockdown of MYC protein expression in several cancer cell lines and in in vivo models.Fundação para a Ciência e Tecnologia - (SFRH/BD/62957/2009); PTDC/BIO/66514/2006; NANOLIGHT-PTDC/QUI-QUI/112597/2009; Silencing the silencers via multifunctional gold nanoconjugates towards cancer therapy - PTDC/BBB-NAN/1812/201

Visualization and Localization of Interventional Devices with MRI by Susceptibility Mapping

Recently, interventional procedures can be performed with the visual assistance of MRI. However, the devices used in these procedures, such as brachytherapy seeds, biopsy needles, markers, and stents, have a large magnetic susceptibility that leads to severe signal loss and distortion in the MRI images and degrades the accuracy of the localization. Right now, there is no effective way to correctly identify, localize and visualize these interventional devices in MRI images. In this dissertation, we proposed a method to improve the accuracy of localization and visualization by generating positive contrast of the interventional devices using a regularized L1 minimization algorithm. Specifically, the spin-echo sequence with a shifted 180-degree pulse is used to acquire high SNR data. A short shift time is used to avoid severe phase wrap. A phase unwrapping method based on Markov Random Field using Highest-Confidence-First algorithm is proposed to unwrap the phase image. Then the phase images with different shifted time are used to calculate the field map. Next, L1 regularized deconvolution is performed to calculate the susceptibility map. With much higher susceptibility of the interventional devices than the background tissue, the interventional devices show positive-contrast in the susceptibility image. Computer simulations were performed to study the effect of the signal-to-noise ratio, resolution, orientation and size of the interventional devices on the accuracy of the results. Experiments were performed using gelatin and tissue phantom with brachytherapy seeds, gelatin phantoms with platinum wires, and water phantom with titanium needles. The results show that the proposed method provide positive contrast images of these interventional devices, differentiate them from other structures in the MRI images, and improves the visualization and localization of the devices

Molecular imaging of abdominal aortic aneurysms

Abdominal aortic aneurysm (AAA) disease is characterised by an asymptomatic, permanent, focal dilatation of the abdominal aorta progressing towards rupture, which confers significant mortality. Patient management and surgical decisions currently rely on aortic diameter measurements via abdominal ultrasound screening. However, AAA rupture can occur at small diameters or may never occur at large diameters. Therefore, there is a need to develop molecular imaging-based biomarkers independent of aneurysm diameter that may help stratify patients with early-stage AAA to reduced surveillance. AAA uptake of [18F]fluorodeoxyglucose on positron emission tomography (PET) has been demonstrated previously; however, its glucose-dependent uptake may overlook other key mechanisms. The cell proliferation marker [18F]fluorothymidine ([18F]FLT) is primarily used in tumour imaging. The aim of the overall study for this thesis was to explore the feasibility of [18F]FLT PET / computed tomography (CT) to visualise and quantify AAA in the angiotensin II (AngII)-infused mouse model. The experiments presented in this thesis revealed increased uptake of [18F]FLT in the 14-day AngII AAA model than in saline controls, followed by a decrease in this uptake at 28 days. Moreover, in line with the in vivo PET/CT findings, Western blotting of aortic tissue revealed increased levels of thymidine kinase-1 (the substrate of [18F]FLT) and nucleoside transporters in the 14-day AngII AAA model than in saline controls, followed by decreased expression levels at 28 days. A pilot experiment further demonstrated that [18F]FLT PET/CT could be used to detect an early therapeutic response to oral imatinib treatment in the AngII AAA model. Therefore, [18F]FLT PET/CT may be a feasible modality to detect and quantify cell proliferation in the AngII AAA murine model. The findings of this thesis are encouraging for the application of [18F]FLT PET/CT in patients with small AAA

Investigating Tissue Heterogeneity using MRI in Prostate Cancer

Multi-parametric MRI, a promising new technique for grading prostate cancer using MRI, classifies a high number of regions as indeterminate. This is a symptom of the wider problem that clinical usage of MRI in prostate cancer only includes basic techniques and does not directly categorise tissue microstructure. This work provides insight into the microstructure of the prostate using a combination of new tissue models and acquisition schemes. Each is tested with the aim of producing a method that is better at detecting and grading prostate cancer. The first section utilises microstructural diffusion models to better quantify tissue heterogeneity in the prostate. The two models investigated provided more information about the heterogeneous nature of the prostate that ADC and showed significant difference between lesions and normal tissue. The next section looks into combining multi-echo T2 (ME-T2) sequences with quantitative tissue modelling called Luminal Water Imaging (LWI). This work produced an optimal LWI fitting technique and acquisition. Then the ability of LWI to detect the PI-RADS v2.0 score of regions of interest was examined, showing that it was able to differentiate between scores better than ADC. This work also showed that LWI can differentiate between tumour and normal tissue with an AUC of 0.81 (p<0.05) when compared to ADC with an AUC of 0.75 (p<0.05) in this dataset. The next section further improves the acquisitions using larger datasets. It showed that correcting for imperfect pulse refocusing could improve on the performance of LWI in detecting PCa. This work also showed that fewer echoes could be used in the acquisition. Neural networks were then used to detect and grade prostate cancer using the data points from both multiple b-value diffusion and ME-T2 decay curves. The neural network’s ability to distinguish between different PIRADS scores was shown to have an AUC of 0.87 (p<0.05) using 32-echo data

Development of Targeted Therapeutics for the Treatment of Glioblastoma

Glioblastoma is the most aggressive cancer of the brain. Despite recent advances in cancer biology and multimodality therapies, such as surgery, radiotherapy and chemotherapy, the outcome of patients with high grade glioma remains fatal. The major drawback of current glioma chemotherapeutics is their inability to cross the blood brain barrier, lack of tumour specificity agents and their consequent side effects. Matrix metalloprotease (MMP) activity is central to cancer development, angiogenesis and invasion. They are highly active in the tumour environment and absent or inactive in normal tissues, therefore they represent viable targets for cancer drug discovery. A better understanding of the role of MMPs in human gliomas could potentially have diagnostic, prognostic and therapeutic implications. This study aims to assess the expression of specific MMPs in preclinical human glioma models and clinical glioma samples; evaluate in silico docking to rationalise substrate binding preferences of homologous MMPs; rationally design MMP-subtype-selective tumour activated prodrugs; and determine the feasibility of targeting MMP-selective anticancer prodrugs conjugated to graphene oxide as a local drug delivery approach for glioblastoma. This study found significant overexpression of MMP-10 in glioma relative to histologically normal brain tissues. Strong correlation was observed between MMP-10 protein and gene expression of glioma cell lines relative to low expression in a normal brain cell line. MMP-10 activity, as measured by fluorogenic substrate cleavage assay, also demonstrated a strong correlation between MMP-10 activity and gene expression levels. Following demonstration of selective overexpression of MMP-10 in glioma, a reiterative in silico proteolytic docking coupled in vitro biochemical assessment was utilised to rationalise functional similarity and differentiate substrate binding selectivity of homologous MMPs. The binding modes of MMP-substrates within the active site of closely related MMPs were able to accurately predict the cleavage subsites by specific MMPs, as confirmed by in vitro cleavage assay. The success of computational and experimental methodology provided a robust tool for identifying MMP-subtype differences and subsequent development of MMP-10 selective peptide prodrugs. MMP-subtype selective and MMP-10 selective prodrugs were designed by rational exploitation of MMP-docked complexes of substrates. Peptide residues were modified to achieve selectivity for MMP-2 and MMP-10 (over MMP-3 and MMP-9) demonstrating predicted cleavage at distinct subsites. This selectivity was further exploited to attain MMP-10 selectivity, over MMP-2, MMP-3 and MMP-9. The rationally designed peptide prodrugs were synthesised and were shown to be preferentially cleaved by MMPs at predicted subsites and demonstrated no activation by engineered-out MMPs, as predicted. Compared to MJ02 (MMP-2 and MMP-10 selective doxorubicin prodrug), MJ04 (MMP-10 selective doxorubicin prodrug) demonstrated selective metabolism by glioma cell lines to release chemotherapeutic agents. This therapeutic approach against glioma cell lines depended upon the involvement of MMPs, confirmed using pharmacological inhibition. MJ04 demonstrated negligible activity in the presence of an MMP-10 selective inhibitor, suggesting MMP-10 selective activation of the prodrug in glioma cells relative to normal glial cells. Following successful development of MMP-10 selective prodrugs, the feasibility of targeting glioma tumour with local delivery of chemotherapeutics from functionalised graphene-oxide tethered prodrug implants, was assessed as a therapeutic strategy to circumvent the blood brain barrier. Graphene oxide conjugated prodrug was synthesised which is shown to be preferentially cleaved in MMP expressing glioma cell lines relative to normal glial cells. This study demonstrates that MMP-10 is overexpressed in glioblastoma and can be used to metabolise anticancer prodrugs that can be activated selectively by local tumour environment