Browsing by Author "Morgan, Sarah"

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    Classification of endocrine resistant breast cancers from transcriptomic datasets using multi-gene signatures
    (Cranfield University, 2012-09) Larionov, Alexey; Cameron, David; Morgan, Sarah
    Breast cancer is the most frequent cancer in women in developed countries. Endocrine treatment is indicated to the majority of breast cancer patients. However, in some cases it does not work despite the current clinical indications. Eventually the resistance may develop in many of those who initially respond. Re-analysis of available breast cancer transcriptomic datasets using new multi-gene signatures associated with endocrine resistance may help to understand and overcome endocrine resistance. The goal of this project was to develop a bioinformatics pipeline to (i) select endocrine resistant cases from the available breast cancer datasets and (ii) classify the selected cases by multiple multi-gene signatures. The pipeline has been successfully designed and applied for classification of endocrineresistant samples from 9 breast cancer datasets using 7 transcriptional signatures. The obtained results have been presented in a dedicated web site. The pipeline consists of:  Procedures for a manually curated selection of relevant datasets and signatures;  Procedures for semi-automatic data pre-processing, allowing cross-platform analysis;  A new, fully automated, classification algorithm (Iterative Consensus PAM). The main features of the developed classification algorithm include:  It is based on un-supervised partitioning;  It allows for “non-classifiable” samples;  The procedure does not require a training set;  The procedure can be used in a cross-platform context (Affymetrix & Illumina). The developed pipeline and web site may constitute a prototype for a future web-hub collecting (i) data on endocrine-resistant breast cancer specimens, (ii) collecting multigene signatures relevant to endocrine resistance and (iii) providing tools to apply the signatures to the data. The web-repository could provide a tool to integrate the data and signatures and to produce new clinical and biological knowledge about endocrine resistance in breast cancer.
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    Development of a quantum dot-encoded microsphere suspension assay for the genotyping of single nucleotide polymorphisms
    (Cranfield University, 2009-03) Thiollet, Sarah; Morgan, Sarah; White, Nicola
    This thesis describes the investigation of quantum dot-doped particle fluorescent technology commercially available for its application to analyte profiling in suspension. The first part of the thesis described the characterisation of the quantum dot-encoded microspheres, QDEMs, developed by Crystalplex (PA, USA). The multiple fluorescence signatures of QDEMs were analysed using microscopy and flow cytometry technology which provided high-content measurements with a single excitation sources and multiple emission wavelength detectors. The sensitivity and stability of the materials was evaluated under typical biomedical conditions encounter in multiple analyte suspension assays. Novel analytical parameters were defined to study QDEM stability and confocal microscopy detection system was used to provide structural and fluorescent imagines of the fluorescent microspheres under various conditions. Composition of the aqueous environment, temperature and physical forces applied to QDEM induced changes in their fluorescent codes and structural properties. Optimal conditions were then defined for the application of the material to biomedical assays. In a second stage, a conjugation method was developed to produce optimised QDEM bioconjugates for the detection of single strand DNA in suspension. The impact of the conjugation buffer, the concentration and the structure of oligonucleotides was evaluated to optimise QDEM bioconjugates. Then, a novel approach was investigated to optimise the hybridisation of ssDNA to QDEM bioconjugates. Experimental design with response surface methodology determined optimum conditions for the hybridisation of oligonucleotides to QDEM surface in suspension array. Finally, the specific hybridisation of ssDNA to QDEM bioconjugates in a small liquid format adapted to single nucleotide polymorphism detection was demonstrated. The work presented here shows the potential of QDEM bioconjugates for suspension array technology and DNA genotyping. Further, this report highlights the challenges that remain for QDEM fluorescent technology to be reliable for biomedical and suspension array applications.
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    Development of a rapid immunoassay for human pathogenic markers
    (Cranfield University, 2006-09) Lawton, Nicola Jane; Turner, Anthony P. F.; Morgan, Sarah; Burgess, Paul J.
    A demand exists for a fast, sensitive, reliable and economical test for pyogenic sepsis that provides a “real time” bed-side assessment. Detection of significant intra-abdominal sepsis can be particularly problematic in the ICU setting and in patients with multi-system organ failure. Lysozyme, first reported by Fleming (1922), is a bacteriolytic enzyme released during phagocytosis. Previous studies have shown significant correlation between lysozyme levels and the presence of intra-abdominal abscess in both animals and humans. A method which determines and quantifies lysozyme as part of an assessment of an acutely ill patient in whom major sepsis is suspected; would significantly aid diagnosis and prescription of the most effective form of treatment. To date measurement of lysozyme has been by turbidometry, with consequent poor sensitivity and reliability. Other methods of assay include fluorescence, radial immunodiffussion and enzyme linked immunosorbent assay (ELISA). This study reports a modified ELISA technique which provides a cheap, sensitive and reliable method of lysozyme determination, producing results in <100 minutes. The ELISA has been tested with ~200 clinical samples provided by the patients at the Great Western Hospital, Swindon. Two ELIFA techniques were also developed for lysozyme and E.coli detection. These techniques also provide a cheap and rapid alternative to the more traditional immunoassays. Results from the ELIFA and mini-ELIFA were obtained qualitatively after only 10 minutes. An SPR detection technique was also devised. The BIAcore 3000 was used to create a biosensor for serum lysozyme using an artificial receptor in the form of an aptamer. This system was tested with clinical serum samples, is reusable and took <80 minutes to immobilise a ligand on a blank sensor and analyse a serum sample for lysozyme. Although further research and development is required on the mini-ELIFA and lysozyme biosensor, the ELISA detection system may prove a useful tool in the diagnosis of sepsis in critically ill patients.
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    Development of new fluorescent silica and multifunctional nanoparticles for bio-imaging and diagnostics
    (Cranfield University, 2011-03) Lemelle, Arnaud; Morgan, Sarah; Tothill, Ibtisam E.
    Silica nanoparticles are effective fluorophore carriers with high potential in imaging, diagnostics, and therapy. The particles are resistant to drastic change of environmental conditions (pH, temperature etc. and insulate the dyes so as to protect them from photobleaching. Silica chemistry is also versatile and affords an easy modification of the particle composition and surface to integrate targeting ligands or to integrate other nanoparticles. Regardless of their advantages, there exists a lack of dye diversity in the literature that is connected to a low affinity for potential tools for biology and medicineThis thesis describes the development of an alternative method for the synthesis of fluorescent silica nanoparticles and their modification to incorporate iron oxide and gold. cont/d.
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    Final thoughts on WWI and WWII legislation, recovery, identification and burial of human remains: best practice, challenges, and recommendations
    (Elsevier, 2021-03-19) Márquez-Grant, Nicholas; Errickson, David; Morgan, Sarah; Ronner, Eva; Giles, Stephanie B.
    The ‘WWI and WWII Symposium: Legislation, Recovery, Identification and Burial of Human Remains’, took place on 13th March 2020 (Márquez-Grant and Errickson, 2021). The event was in the form of a round table discussion with participating specialists who focus on the forensic recovery and identification of war casualties, particularly with a focus on Europe. Although the event saw a large amount of knowledge exchange, the discussion went far beyond those who attended the session. As a result, this Special Issue in ‘Forensic Science International’ is aimed at disseminating the discussion to a wider number of individuals while incorporating further views and input from specialists who could not be in attendance on the day.
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    Investigating the impact of NHS based ovarian cancer screening
    (Cranfield University, 2010-02) Nicholson, S. M.; Morgan, Sarah; Sehdev, K.
    the UK ovarian cancer is the fifth most common cancer in females and after uterine cancer, the second most common gynaecological cancer. There were 6,596 new cases diagnosed in the UK in 2006. The majority of women who develop ovarian cancer have few symptoms until the cancer has spread. A systematic review of published literature was performed to include randomised control trials, case control or cohort studies. It is apparent from the literature on ovarian cancer screening that internationally extensive research is performed however, there is lack of consensus on who to offer screening to, and the most efficacious way of offering it. Annual screening was found to be inadequate for early cancer detection as several studies report advanced stage disease or found that women were developing symptoms in the interim period of screening visits. The retrospective studies performed at Milton Keynes Hospital demonstrated that ovarian cancer affects a wide age range with many women having no family history of ovarian or breast cancer. Many cases were found to have early stage ovarian cancer however, the largest group of women were found to have extensive metastatic disease at time of diagnosis. 80% of cases reviewed experienced abdominal or pelvic pains often with distension. Five patients were found to have a CA125 value in the normal range, one of which had advanced disease, indicating the limitations of this biomarker. The impact and costs associated with screening in the NHS setting vary considerably with inclusion criteria used. The UK National Screening Committee will have to decide once the findings of UKCTOCS are published in 2010/11 as to the cost benefit of offering NHS based ovarian cancer screening. An annual cost of at least £1.3 million should be expected per NHS trust, in addition to individual trusts needs for equipment, staff and additional facilities required to offer such screening.
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    Investigation of the effect of structured hyaluronic acid surfaces on cell proliferation and expression of HA cellular receptors:CD44 and RHAMM
    (Cranfield University, 2011-03) Marques, Ana Catia Ferrao; Morgan, Sarah; Cullen, David C.
    Hyaluronic acid (HA) is one of the major components of the extracellular matrix; and may exhibit different biological functions, dependent on polymer molecular weight (MW). The signalling events performed by HA are mediated through interactions with its main cell receptors: CD44 and RHAMM. However, the direct effect between the HA MW and the expression of CD44 and RHAMM remains unclear. This study aimed to investigate whether different HA polymer MW alters the proliferation of tumour-derived cell lines, and whether different HA-sized has an effect on the regulation of the expression of CD44 and RHAMM. In order to determine size-specific responses of tumour cells of defined fragment MW, this investigation was undertaken using HA-tethered culture surfaces. Four surfaces were constructed, coated with polymers of different MWs. HA (4, 234, 2590 kDa) and an oligomer mixture were tethered onto an aminosilane (AHAPTMS)-treated glass surfaces using a carbodiimide reaction. Surfaces were analysed using a toolbox of in situ characterisation techniques, including wettability measurements, QCM, AFM and confocal microscopy. Using the constructed surfaces was demonstrated that HA-polymer MW modulates cell proliferation of human bladder (RT112 and T24) and prostate (PC3 and PNT1A) cell lines, with low HA MW (HA4) increasing proliferation, whereas a decrease is seen in the presence of medium (HA234) and high MW fragments (HA2590). The proliferation stimulus performed by HA was found to be phenotype dependent, with HA4 surfaces stimulating an increased proliferation in those less invasive cell lines (T24 and PNT1A), while HA234 and HA2590 inducing a sharper decrease in the most malignant tumour cell lines (RT112 and PC3). It was also demonstrated that the regulation of CD44 and RHAMM transcripts expression appears to be phenotype dependent but not HA-MW dependent. HA down-regulates CD44 and RHAMM in the most malignant cell lines; with up-regulation of the expression of the cell receptors in the less invasive cell lines. In addition, the presence of exogenous HA was shown to be involved in the regulation of the expression of CD44 variants expression. The results obtained for the CD44 and RHAMM protein expression were also found to be correlated with the obtained transcripts expression. However, the significance of these findings in tumourigenesis remains unclear. Findings from this investigation may help in the design and development of biocompatible implants with controlled surface properties to be used in cancer therapeutics; with medium and large HA polysaccharides being potential biopolymer candidates, useful for the development of novel therapies for highly invasive cancer. In addition, implications from this work can serve as a base for future research, and can lead to ideas for drugs and methods to be used in cancer therapeutic approaches.
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    Towards objective endoscopic diagnosis of Barrett's associated early neoplasia using fibre-optic Raman Spectroscopy
    (Cranfield University, 2012-08) Almond, Laurence Maximilian; Kendall, Catherine; Hutchings, J.; Morgan, Sarah; Barr, H.
    This translational research evaluates a novel, custom-built Raman probe for potential application as an in vivo diagnostic tool in the oesophagus. Raman spectroscopy (RS) is a well established analytical technique which is capable of probing the biochemical changes associated with neoplastic progression in oesophageal tissue. RS relies on measurement of subtle inelastic scattering signals following monochromatic laser excitation. Clinical utilisation of RS within hollow organs requires accurate collection and transmission of signal through fibre-optic cables. This research aims to evaluate the ability of a custom built fibre-optic Raman probe, in conjunction with multivariate classification models, to differentiate between benign and neoplastic oesophageal pathologies ex vivo. The need for spectral stability and reproducibility are addressed, as are difficulties associated with multisystem reliability. In addition, the biochemical basis of spectral classification is evaluated and discussed. Cont/d.