Soft tissue sarcoma: biology and therapeutic correlates

Soft tissue sarcomas (STS) comprise a heterogenenous group of greater than 50 malignancies of putative mesenchymal cell origin and as such they may arise in diverse tissue types in various anatomical locations throughout the whole body. Collectively they account for approximately 1% of all human malignancies yet have a spectrum of aggressive behaviours amongst their subtypes. They thus pose a particular challenge to manage and remain an under investigated group of cancers with no generally applicable new therapies in the past 40 years and an overall 5-year survival rate that remains stagnant at around 50%. From September 2000 to July 2006 I undertook a full time post-doctoral level research fellowship at the MD Anderson Cancer Center, Houston, Texas, USA in the department of Surgical Oncology to investigate the biology of soft tissue sarcoma and test novel anti- sarcoma adenovirus-based therapy in the preclinical nude rat model of isolated limb perfusion against human sarcoma xenografts. This work, in collaboration with colleagues as indicated herein, led to a number of publications in the scientific literature furthering our understanding of the malignant phenotype of sarcoma and reported preclinical studies with wild-type p53, in a replication deficient adenovirus vector, and oncolytic adenoviruses administered by isolated limb perfusion. Additional collaborative and pioneering preclinical studies reported the molecular imaging of sarcoma response to systemically delivered therapeutic phage RGD-4c AAVP. Doxorubicin chemotherapy is the single most active broadly applicable anti-sarcoma chemotherapeutic yet only has an approximate 30% overall response rate with additional breakthrough tumour progression and recurrence after initial chemo-responsiveness further problematic features in STS management. Doxorubicin is a substrate for the multi- drug resistance (mdr) gene product p-glycoprotein drug efflux pump and exerts its main mode of action by induction of DNA double-strand breaks during the S-phase of the cell cycle. Two papers in my thesis characterise different aspects of chemoresistance in sarcoma. The first shows that wild-type p53 suppresses Protein Kinase Calpha (PKCα) phosphorylation (and activation) of p-glycoprotein by transcriptional repression of PKCα through a Sp-1 transcription factor binding site in its -244/-234 promoter region. The second paper demonstrates that Rad51 (a central mediator of homologous recombination repair of double strand breaks) has elevated levels in sarcoma and particularly in the S- G2 phase of the cell cycle. Suppression of Rad51 with small interfering RNA in sarcoma cell culture led to doxorubicin chemosensitisation. Reintroduction of wild-type p53 into STS cell lines resulted in decreased Rad51 protein and mRNA expression via transcriptional repression of the Rad51 promoter through increased AP-2 binding. In light of poor response rates to chemotherapy, escape from local control portends a poor prognosis for patients with sarcoma. Two papers in my thesis characterise aspects of sarcoma angiogenesis, invasion and metastasis. Human sarcoma samples were found to have high levels of matrix metalloproteinase-9 (MMP-9) with expression levels that correlated with p53 mutational status. MMP-9 is known to degrade extracellular collagen, contribute to the control of the angiogenic switch necessary in primary tumour progression and facilitate invasion and metastasis. Reconstitution of wild-type p53 function led to decreased levels of MMP-9 protein and mRNA as well as zymography-assessed MMP-9 proteolytic activity and decreased tumour cell invasiveness. Reintroduction of wild-type p53 into human sarcoma xenografts in-vivo decreased tumour growth and MMP-9 protein expression. Wild-type p53 was found to suppress mmp-9 transcription via decreased binding of NF-κB to its -607/-595 mmp-9 promoter element. Studies on the role of the VEGF165 in sarcoma found that sarcoma cells stably transfected with VEGF165 formed more aggressive xenografted tumours with increased vascularity, growth rate, metastasis, and resistance to chemotherapy. Use of the anti-VEGFR2 antibody DC101 enhanced doxorubicin sensitivity at sub-conventional dosing, inhibited tumour growth, decreased development of metastases, and reduced tumour micro-vessel density while increasing the vessel maturation index. These effects were explained primarily through effects on endothelial cells (e.c.s), rather than the tumour cells per se, where DC101 induced e.c. sensitivity to doxorubicin and suppressed e.c. production of MMPs. The p53 tumour suppressor pathway is the most frequently mutated pathway in sarcoma. Recapitulation of wild-type p53 function in sarcoma exerts a number of anti-cancer outcomes such as growth arrest, resensitisation to chemotherapy, suppression of invasion, and attenuation of angiogenesis. Using a modified nude rat-human sarcoma xenograft model for isolated limb perfusion (ILP) delivery of wild-type p53 in a replication deficient adenovirus vector I showed that functionally competent wild-type p53 could be delivered to and detected in human leiomyosarcoma xenografts confirming preclinical feasibility - although not efficacious due to low transgene expression. Viral fibre modification to express the RGD tripeptide motif led to greater viral uptake by sarcoma cells in vitro (transductional targeting) and changing the transgene promoter to a response element active in cells with active telomerase expression restricted the transgene expression to the tumour intracellular environment (transcriptional targeting). Delivery of the fibre-modified, selectively replication proficient oncolytic adenovirus Ad.hTC.GFP/ E1a.RGD by ILP demonstrated a more robust, and tumour-restricted, transgene expression with evidence of anti-sarcoma effect confirmed microscopically. Collaborative studies using the fibre modified phage RGD-4C AAVP confirmed that systemic delivery specifically, efficiently, and repeatedly targets human sarcoma xenografts, binds to αv integrins in tumours, and demonstrates a durable, though heterogeneous, transgene expression of 1-4 weeks. Incorporation of the Herpes Simplex Virus thymidine kinase (HSVtk) transgene into RGD-4C AAVP permitted CT-PET spatial and temporal molecular imaging in vivo of transgene expression and allowed quantification of tumour metabolic activity both before and after interval administration of a systemic cytotoxic with predictable and measurable response to treatment before becoming apparent clinically. These papers further the medical and scientific community’s understanding of the biology of soft tissue sarcoma and report preclinical studies with novel and promising anti- sarcoma therapeutics.

Volunteering for the Commonwealth Games: what can realist synthesis contribute to health policy making?

The aim of this thesis was to investigate, using the real-time test case of the 2014 Commonwealth Games, whether the realist synthesis methodology could contribute to the making of health policy in a meaningful way. This was done by looking at two distinct research questions: first, whether realist synthesis could contribute new insights to the health policymaking process, and second, whether the 2014 Commonwealth Games volunteer programme was likely to have any significant, measurable, impact on health inequalities experienced by large sections of the host population. The 2014 Commonwealth Games legacy laid out ambitious plans for the event, in which it was anticipated that it would provide explicit opportunities to impact positively on health inequalities. By using realist synthesis to unpick the theories underpinning the volunteer programme, the review identifies the population subgroups for whom the programme was likely to be successful, how this could be achieved and in what contexts. In answer to the first research question, the review found that while realist methods were able to provide a more nuanced exposition of the impacts of the Games volunteer programme on health inequalities than previous traditional reviews had been able to provide, there were several drawbacks to using the method. It was found to be resource-intensive and complex, encouraging the exploration of a much wider set of literatures at the expense of an in-depth grasp of the complexities of those literatures. In answer to the second research question, the review found that the Games were, if anything, likely to exacerbate health inequalities because the programme was designed in such a way that individuals recruited to it were most likely to be those in least need of the additional mental and physical health benefits that Games volunteering was designed to provide. The following thesis details the approach taken to investigate both the realist approach to evidence synthesis and the likelihood that the 2014 Games volunteer programme would yield the expected results.

Ecological drivers of a vector borne pathogen: distribution and abundance of Borrelia burgdorferi sensu lato and its vector Ixodes ricinus in Scotland

Vector-borne disease emergence in recent decades has been associated with different environmental drivers including changes in habitat, hosts and climate. Lyme borreliosis is among the most important vector-borne diseases in the Northern hemisphere and is an emerging disease in Scotland. Transmitted by Ixodid tick vectors between large numbers of wild vertebrate host species, Lyme borreliosis is caused by bacteria from the Borrelia burgdorferi sensu lato species group. Ecological studies can inform how environmental factors such as host abundance and community composition, habitat and landscape heterogeneity contribute to spatial and temporal variation in risk from B. burgdorferi s.l. In this thesis a range of approaches were used to investigate the effects of vertebrate host communities and individual host species as drivers of B. burgdorferi s.l. dynamics and its tick vector Ixodes ricinus. Host species differ in reservoir competence for B. burgdorferi s.l. and as hosts for ticks. Deer are incompetent transmission hosts for B. burgdorferi s.l. but are significant hosts of all life-stages of I. ricinus. Rodents and birds are important transmission hosts of B. burgdorferi s.l. and common hosts of immature life-stages of I. ricinus. In this thesis, surveys of woodland sites revealed variable effects of deer density on B. burgdorferi prevalence, from no effect (Chapter 2) to a possible ‘dilution’ effect resulting in lower prevalence at higher deer densities (Chapter 3). An invasive species in Scotland, the grey squirrel (Sciurus carolinensis), was found to host diverse genotypes of B. burgdorferi s.l. and may act as a spill-over host for strains maintained by native host species (Chapter 4). Habitat fragmentation may alter the dynamics of B. burgdorferi s.l. via effects on the host community and host movements. In this thesis, there was lack of persistence of the rodent associated genospecies of B. burgdorferi s.l. within a naturally fragmented landscape (Chapter 3). Rodent host biology, particularly population cycles and dispersal ability are likely to affect pathogen persistence and recolonization in fragmented habitats. Heterogeneity in disease dynamics can occur spatially and temporally due to differences in the host community, habitat and climatic factors. Higher numbers of I. ricinus nymphs, and a higher probability of detecting a nymph infected with B. burgdorferi s.l., were found in areas with warmer climates estimated by growing degree days (Chapter 2). The ground vegetation type associated with the highest number of I. ricinus nymphs varied between studies in this thesis (Chapter 2 & 3) and does not appear to be a reliable predictor across large areas. B. burgdorferi s.l. prevalence and genospecies composition was highly variable for the same sites sampled in subsequent years (Chapter 2). This suggests that dynamic variables such as reservoir host densities and deer should be measured as well as more static habitat and climatic factors to understand the drivers of B. burgdorferi s.l. infection in ticks. Heterogeneity in parasite loads amongst hosts is a common finding which has implications for disease ecology and management. Using a 17-year data set for tick infestations in a wild bird community in Scotland, different effects of age and sex on tick burdens were found among four species of passerine bird (Chapter 5). There were also different rates of decline in tick burdens among bird species in response to a long term decrease in questing tick pressure over the study. Species specific patterns may be driven by differences in behaviour and immunity and highlight the importance of comparative approaches. Combining whole genome sequencing (WGS) and population genetics approaches offers a novel approach to identify ecological drivers of pathogen populations. An initial analysis of WGS from B. burgdorferi s.s. isolates sampled 16 years apart suggests that there is a signal of measurable evolution (Chapter 6). This suggests demographic analyses may be applied to understand ecological and evolutionary processes of these bacteria. This work shows how host communities, habitat and climatic factors can affect the local transmission dynamics of B. burgdorferi s.l. and the potential risk of infection to humans. Spatial and temporal heterogeneity in pathogen dynamics poses challenges for the prediction of risk. New tools such as WGS of the pathogen (Chapter 6) and blood meal analysis techniques will add power to future studies on the ecology and evolution of B. burgdorferi s.l.

LHC main dipole magnet circuits: sustaining near-nominal beam energies

Crossing the Franco-Swiss border, the Large Hadron Collider (LHC), designed to collide 7 TeV proton beams, is the world's largest and most powerful particle accelerator the operation of which was originally intended to commence in 2008. Unfortunately, due to an interconnect discontinuity in one of the main dipole circuit's 13 kA superconducting busbars, a catastrophic quench event occurred during initial magnet training, causing significant physical system damage. Furthermore, investigation into the cause found that such discontinuities were not only present in the circuit in question, but throughout the entire LHC. This prevented further magnet training and ultimately resulted in the maximum sustainable beam energy being limited to approximately half that of the design nominal, 3.5-4 TeV, for the first three years of operation (Run 1, 2009-2012) and a major consolidation campaign being scheduled for the first long shutdown (LS 1, 2012-2014). Throughout Run 1, a series of studies attempted to predict the amount of post-installation training quenches still required to qualify each circuit to nominal-energy current levels. With predictions in excess of 80 quenches (each having a recovery time of 8-12+ hours) just to achieve 6.5 TeV and close to 1000 quenches for 7 TeV, it was decided that for Run 2, all systems be at least qualified for 6.5 TeV operation. However, even with all interconnect discontinuities scheduled to be repaired during LS 1, numerous other concerns regarding circuit stability arose. In particular, observations of an erratic behaviour of magnet bypass diodes and the degradation of other potentially weak busbar sections, as well as observations of seemingly random millisecond spikes in beam losses, known as unidentified falling object (UFO) events, which, if persist at 6.5 TeV, may eventually deposit sufficient energy to quench adjacent magnets. In light of the above, the thesis hypothesis states that, even with the observed issues, the LHC main dipole circuits can safely support and sustain near-nominal proton beam energies of at least 6.5 TeV. Research into minimising the risk of magnet training led to the development and implementation of a new qualification method, capable of providing conclusive evidence that all aspects of all circuits, other than the magnets and their internal joints, can safely withstand a quench event at near-nominal current levels, allowing for magnet training to be carried out both systematically and without risk. This method has become known as the Copper Stabiliser Continuity Measurement (CSCM). Results were a success, with all circuits eventually being subject to a full current decay from 6.5 TeV equivalent current levels, with no measurable damage occurring. Research into UFO events led to the development of a numerical model capable of simulating typical UFO events, reproducing entire Run 1 measured event data sets and extrapolating to 6.5 TeV, predicting the likelihood of UFO-induced magnet quenches. Results provided interesting insights into the involved phenomena as well as confirming the possibility of UFO-induced magnet quenches. The model was also capable of predicting that such events, if left unaccounted for, are likely to be commonplace or not, resulting in significant long-term issues for 6.5+ TeV operation. Addressing the thesis hypothesis, the following written works detail the development and results of all CSCM qualification tests and subsequent magnet training as well as the development and simulation results of both 4 TeV and 6.5 TeV UFO event modelling. The thesis concludes, post-LS 1, with the LHC successfully sustaining 6.5 TeV proton beams, but with UFO events, as predicted, resulting in otherwise uninitiated magnet quenches and being at the forefront of system availability issues.