Qatar Foundation Annual Research Forum Volume 2012 Issue 1

Background: The mammalian proprotein convertases (PCs) constitute a family of nine secretory serine proteases related to bacterial subtilisin and yeast kexin. Seven of them (PC1/3, PC2, furin, PC4, PC5/6, PACE4 and PC7) activate cellular and pathogen precursor proteins by cleavage at single or paired basic residues, while SKI-1/S1P and PCSK9 regulate cholesterol/lipid homeostasis via cleavage at non-basic residues or through induced degradation of receptors. PCs are now considered attractive targets for the development of powerful novel therapeutics. In this poster presentation, I will summarize the physiological functions and pathological implications of the PCs and discuss proposed strategies to control some of their activities, including their therapeutic application and validation in selected disease states. Objectives: The concept of the cleavage of precursor proteins to generate active products was born 47 years ago and the cognate convertases were identified during a 13-year period that ended in 2003 with the identification of PCSK9. Since the discovery of the PCs, efforts have been deployed to identify specific functions of PCs in animal models and humans in both health and disease and they have been implicated in a wide variety of cellular processes that regulate both body homeostasis and multiple disease states. While most PCs exert their functions through cleavage of substrates either at basic or non-basic amino acids, PCSK9 only requires its enzymatic activity to autocatalytically process its prosegment in the endoplasmic reticulum, and is secreted as an inactive protease. The challenging identification of safe orally active small molecule inhibitors of some of the convertases, especially PCSK9, is definitively a future goal that should be pursued vehemently. Conclusions: The use of biologics and desirable automated injection procedures or minimally invasive methods may be the future for effective PC-based therapies. The future is indeed bright and awaits innovative and practical approaches to target these exciting and multifunctional enzymes. The topics discussed here will encourage the investigation and development of potent and effective PC-inhibitors/silencers, and minimally invasive procedures for delivery to patients, which would be highly beneficial in the clinical treatment of diseases in which PCs play a key role.

Background: The recent approval by the FDA of the autologous, cell-based vaccine Provenge was hailed as a major advance for the treatment of advanced prostate cancer (PCa) and reinvigorated interest in the field of PCa immunotherapy. Peptide-based vaccines represent a viable, cost-effective formulation in the field of cancer vaccine development. This approach has been used successfully to treat melanoma where vaccination with gp100-derived peptide in combination with IL-2 gave a 6.7 month improvement in overall survival compared to IL-2 alone. Objectives: Our goal was to identify immunogenic epitopes from gene rearrangement products and tumor coding mutations to generate vaccines for prostate cancer immunotherapy. Methods: We used a 3-step, in silico/in vitro/in vivo approach to identify HLA-A2.1-restricted, immunogenic epitopes derived from the highly prostate tumor-specific antigen ERG, a component of the TMPRSS2:ERG gene fusion that occurs in about 50% of PCa cases. We designed longer epitopes that exhibit helper function through activation of CD4 T lymphocytes. We screened RNAseq data from prostate tumors to identify potential immunogenic epitopes that rise from coding mutations. Predicted epitopes are tested in humanized mice for immunogenicity. Anti-tumor effect of epitope-specific cytotoxic lymphocytes is tested against human prostate tumor cell lines. Results: We have identified several epitopes from ERG that induced a strong immune response in humanized HLA-A2.1+ mice and overcame peripheral tolerance in prostate specific ERG-expressing TRAMP-HLA-A2.1-ERG+ mice. Additionally, we have designed long peptides that target both MHC-I and MHC-II molecules and overcome the need for helper peptides. These immunogenic epitopes are naturally processed and presented by tumor cells to mediate cytotoxicity. Finally, we used RNAseq to identify a high number of tumor-specific, panHLA-customized, coding mutations, including those from KRas oncogene, that exhibit immunogenicity in vivo. Conclusion: Our findings provide proof of concept for peptide-based vaccines that are tailored to the tumor's molecular profile, and lay the ground for future development of personalized vaccines for clinical use.

Background and Aims: Tumor suppressor proteins (TSPs) are inactivated by many different mechanisms, including nuclear exclusion by the chromosome region maintenance protein (CRM-1). Increased tumor levels of CRM-1 have been correlated with poor prognosis of patients with different cancers, making it a therapeutic target. We have developed selective inhibitors of nuclear export (SINEs) that bind to CRM-1 to irreversibly inhibit its ability to export proteins. Here we investigated our new class of SINEs in multiple tumor models. Methods: We studied the effects of SINE analogs in a panel of pancreatic, colon, triple-negative breast cancer (TNBC), prostate, non Hodgkin's lymphoma (NHL) cell lines and non-transformed/normal cells using proliferation, apoptosis, immunoblot, co-immunoprecipitation, small inhibitor (Si)-RNA, and fluorescence microscopy analyses. The effects of the SINEs were also investigated in mice with subcutaneous, orthotopic tumors and in disseminated liquid tumor models. Results: SINEs (KPT-185, KPT-127, KPT-205, and KPT-227) inhibited proliferation and promoted apoptosis of both solid liquid cancer cells, but did not affect normal lymphocytes or immortalized non-transformed cells. The nuclei of cells incubated with KPT-185 accumulated major TSPs such as p53, p73, p27, FOXO, p73, and prostate apoptosis response 4 (PAR-4) and inhibited interactions between CRM-1 and these proteins. Mutations in the region of CRM-1 that binds to SINEs (Cys-528), or siRNA knockdown of TSPs, prevented the ability of KPT-185 to block proliferation and induce apoptosis of cancer cells. Oral administration of the KPT SINEs to mice reduced growth of subcutaneous, orthotopic and disseminated xenograft tumors without major toxicity. Analysis of tumor remnants showed that KPT-SINE disrupted the interaction between CRM-1 and TSP, activated TSP function, and reduced proliferation of tumor cells. Conclusion: We identified SINEs that inhibit CRM-1 and promote nuclear accumulation of tumor suppressor proteins in multiple tumor models. Oral administration of the drug to mice reduces growth of xenograft tumors. Based on our solid preliminary studies a phase I clinical trial has been initiated for both solid tumors and hematological malignancies. Our results provide conclusive evidence in support of a global therapy for different cancers that involves targeted inhibition of nuclear export protein function and warrants advanced clinical investigations.

Background: Self-assembly and self-organization processes offer a powerful strategy for the design of nanomaterials from the ground up with predefined dimensions and properties. Central to these approaches is the design and synthesis of molecules with a built-in ability to undergo a hierarchical sequence of supramolecular reactions, culminating with the formation of a well-defined functional superstructure. The rosette nanotubes (RNTs) are a new class of biocompatible organic nanomaterials with tunable dimensions and properties. They are obtained through the hierarchical self-assembly of small synthetic organic molecules. They can be readily tailored to target and kill cancerous cells. Objectives: Our aim is to address the following issues: (i) extent to which the RNTs can capture and deliver siRNA to a tumour while retaining their activity, (ii) advantages and/or limitations of RNTs compared to clinically tested drug delivery systems (DDS), (iii) effectiveness of RNT-based formulations in cancer treatment, (iv) specificity and real-time tracking of the RNT DDS, (v) toxicity profile of the new RNT DDS, (vi) identification of optimal cancer targets for the RNT DDS, and (vii) categorization of the therapeutic advantages/challenges of this system in animal models. Methods: We have designed a family of RNTs and characterized them chemically and structurally. We have also tested their ability to capture siRNA and deliver it to cancer cells. Results: The binding efficiency was shown to be a function of RNT/siRNA ratio, net charge, and local cationic density. These formulations were reproducible at different ionic strength media and were shown to protect siRNA from degradation by serum nucleases. Moreover, the presence of siRNA also played a role in dictating the supramolecular shape of the nanocarrier, which may reflect in-cell uptake and the resulting silencing process. Fluorescence microscopy showed that Caco-2 cells can take up RNT derived assemblies very readily within 4 hours and retain siRNA up to 72 hours. Silencing experiments showed a dose-dependent reduction in VEGF protein levels secreted by Caco-2 cells reaching approximately 40% reduction at 20 nM siRNA. Conclusions: We have shown that the RNTs are effective oligonucleotide carriers. Future studies will involve animal studies and further optimization of the observed therapeutic effect.

Background: The multi-disciplinary team (MDT) coordinator’s role is relatively new and as such is evolving. What is apparent is that the coordinator's work is pivotal to the effectiveness and efficiency of an MDT. Objectives: This study aimed to assess the views and needs of MDT-coordinators. Methods: Views of MDT-coordinators were evaluated through an online survey that covered their current practice and role, MDT chairing, opinions on how to improve MDT meetings, and coordinators' educational/training needs. Results: 265 coordinators responded to the survey. More than one third of the respondents felt that the job plan does not reflect their actual duties. It was reported that medical members of the MDT always contribute to case discussions. 66.9% of the respondents reported that MDTs are chaired by surgeons. The majority reported having training on data management and IT skills but more than 50% reported that further training is needed in areas of oncology, anatomy and physiology, audit and research, peer-review, and leadership skills (Figure 1) Conclusions: The MDT coordinator’s role is central to the care of cancer patients. The study reveals areas of training requirements that remain unmet. Improving the resources and training available to MDT-coordinators can give them an opportunity to develop the required additional skills and contribute to improved MDT performance and ultimately cancer care. MDTs in the developmental stage should benefit from the experience of well-established organisations to enhance the cancer care. Finally, this study acknowledges the recent launch of a new e-learning training programme for MDT coordinators that is an important resource for these cancer key workers.

Networks of dynamical systems occur in diverse areas of engineering, such as distributed computation, automated vehicular formations, and power systems networks. We investigate the interplay between network coherence and the network's interconnection topology. In such networks, synchronization or more general coherence under stochastic uncertainty is an important measure of performance. For example, in power systems this notion corresponds to phase and frequency coherence of multiple generators (the lack of which may lead to so-called inter-area oscillations), while in vehicular formations this notion corresponds to how well vehicles are collectively tracking their commanded trajectories. We study abstractions of all of the above problems as distributed/cooperative control problems. We investigate the asymptotic limits of performance when network sizes become large as a function of the networks' topologies. This has important implications for the design of future highly-distributed-generation power networks, as well as large vehicular formation schemes such as those in proposed automated highway systems. This talk will specifically address the notion of network coherence under stochastic disturbances, and its dependence on network topology and various notions of network dimension. Regular lattices and fractal networks provide case studies with both integer and fractional dimension. We give asymptotic lower bounds on network disorder and show its dependence on both the complexity of individual node dynamics, as well as network dimension. It turns out that higher connectivity improves coherence, while more complex node dynamics can hinder it. However, in all cases there is a critical network dimension above which purely local interactions can lead to the emergence of global order. We outline the connections between these results and those on the statistical mechanics of harmonic solids. For future highly-distributed-generation power networks, we quantify the cost of synchronization in terms of resistive line losses due to the power flow needed to achieve this synchrony. We show that this cost scales unboundedly with the number of generators in the network and is independent of the underlying connection topology. This result is a further argument for the use of information communication rather than only power flows to enhance synchrony in such large networks.

Background: A techno-economic analysis has been performed for a coal-fired power plant retrofitted with solvent-based post-combustion carbon capture (PCC) technology where thermal energy is partially supplied by solar thermal collectors. The plant is compared with a generic PCC plant where all the thermal energy is provided by steam bled from the steam cycle. A suite of solar thermal collectors which include flat plate collectors, compound parabolic collectors, linear Fresnel collectors, evacuated tube collectors (ETCs) and parabolic trough collectors (PTCs) have each been tested for their viability. The plant has been simulated for several different locations in Australia: Sydney, Townsville and Melbourne. Objectives: This study investigates the integration of solar thermal energy in the energy mix of a power plant by using it to partially compensate for the debilitating energy penalty burdened by the introduction of the carbon capture process. Methods: The overall system consists of three subsystems: power plant, PCC plant and solar collector field. A base case scenario is studied in which there is no heat integration between the three subsystems and is compared to a system with heat integration. Additionally, incentives such as renewable energy certificates (RECs), carbon tax/credits and government subsidies have been considered in the economic model and a sensitivity analysis has been performed for each scenario of incentives for all five solar collector technologies at the three locations. Results: The ETC is found to be the best performer amongst solar collectors when the three subsystems have good heat integration while the PTC is the best performer in the case of no heat integration. The best location for the solar-assisted PCC (SPCC) plant is found to be Sydney. Conclusions: The SPCC plant is only economically viable in Sydney and Townsville once incentives such as RECs, carbon tax and subsidies are taken into account. By the use of solar energy and the available government incentives for their deployment, the cost of carbon capture is shown to be reduced.

In recent years, concentration has been adopted as a promising strategy to high $/W ratio of photovoltaic energy conversion. In concentrated photovoltaics, the Sun's energy is focused into a smaller area allowing for the conversion of sunlight into electricity using only a small low-cost photovoltaic cell. Conventional solar concentrators, which use III-V are, however, costly to produce. Ideally, the material should perform well under high concentration and be affordable. We propose to construct solar cells based on an excellent candidate materials system, InGaN, whose band gap can be adjusted from 0.7 eV to 3.4 eV as the indium content is reduced. Recent progress has resulted in InGaN solar cells with 97% internal quantum efficiency and 57% external quantum efficiency with an active region only 60 nm thick. This work demonstrates that electron-hole pairs are very efficiently collected in InGaN materials and the absorption is very strong at the band gap. The toughness of the nitride materials translates into its excellent performances under harsh environments: high temperature and humidity and high concentration. Georgia Tech-CNRS and their partners have developed unique lift-off technologies that dramatically lower nitride cost as a result of the ability to reuse the substrates used for the growth of nitrides. These lift-off technologies are also favorable for integration of InGaN cells with building materials like glass or metal, or with other solar cells, such as those made of silicon. In this presentation InGaN solar cells progress and results will be presented.

The evaluation of the contaminant transport is dictated by the Federal Soil Protection Regulation (BBodSchV, 1999) for sites that are suspected to endanger the groundwater. Vulnerability maps are often used for this evaluation. However, vulnerability maps consider the intrinsic vulnerability according to different methods taking some soil properties into account. Such qualitative method is not accurate when it comes to calculate the contaminant transport and looking at the specific vulnerability. Within the framework of a research project, a new investigation concept for the prediction of contaminants input into the groundwater was developed. This concept considers the estimation of the emission (E) of the contaminants, i.e., the time dependent amount and concentration of the leachate of the contamination source. The amount of leachate can be estimated by the infiltration of the groundwater recharge for every hydrological year using hydrological parameters. The expected concentration can be obtained from elution tests. In a second step, the transmission (T), i.e., the pollutant transport through the unsaturated zone into the groundwater is evaluated. This evaluation considers the transport mechanisms advection, diffusion and the retardation potential of the transmission zone. As a result, the immission (I) into the groundwater, the amount and concentration of the contaminants input can be estimated. Finally, it is important to evaluate the sensitivity of the system by classifying the groundwater according to the source value. This evaluation technique comprises a characterization of the site and an estimation of the contamination potential by conducting laboratory and in-situ tests and a numerical simulation modelling involving iteration for a contaminant mass balance. In this paper, a new testing method in a diffusion cell for the determination of the characteristic parameters for the transport mechanisms including the retardation potential is described and an evaluation concept for the contaminant transport based on the testing results is presented and discussed.