Difference between revisions of "Team:SPSingapore/Project"

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  <li><a href='https://2015.igem.org/Team:SPSingapore/'><span>Home</span></a></li>
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<li class = 'active'><a href='https://2015.igem.org/Team:SPSingapore/'><span>Home</span></a></li>
  <li><a href='https://2015.igem.org/Team:SPSingapore/Team'><span>Team</span></a></li>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Team'><span>Team</span></a>
  <li><a href='https://2015.igem.org/Team:SPSingapore/Project'><span>Project</span></a></li>
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<ul>
  <li><a href='https://2015.igem.org/Team:SPSingapore/Protocol'><span>Protocol</span></a></li>
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<li><a href="https://2015.igem.org/Team:SPSingapore/Team">Overview</a></li>
  <li><a href='https://2015.igem.org/Team:SPSingapore/Parts'><span>Parts</span></a></li>
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<li><a href="https://igem.org/Team.cgi?id=1804">Official Profile</a></li>
  <li><a href='https://2015.igem.org/Team:SPSingapore/Notebook'><span>Notebook</span></a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Team Bios">Team Bios</a></li>
  <li class = 'active'><a href='https://2015.igem.org/Team:SPSingapore/Practices'><span>Human Practices</span></a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Mentors">Mentors</a></li>
  <li class='last'><a href='https://2015.igem.org/Team:SPSingapore/Safety'><span>Safety</span></a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Attributions">Attributions</a></li>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Project'><span>Project</span></a>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Project'>Overview</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Invasin">Invasin + Listerolysin</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/ESAQS">esa Quorum Sensing</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Anaerobic Promoter">Anaerobic Promoter</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Parts">Parts</a></li>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Notebook'><span>Notebook</span></a>
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<li><a href="https://2015.igem.org/Team:SPSingapore/Protocol">Protocols</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Notebook">Entries</a></li>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Practices'><span>Human Practices</span></a>
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<li><a href="https://2015.igem.org/Team:SPSingapore/Practices">Overview</a></li>
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<li><a href="https://2015.igem.org/Team:SPSingapore/Workshop">Workshop</a></li>
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<li><a href="https://2015.igem.org/Team:SPSingapore/Workshop Materials">Workshop Materials</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Interview">Consultations</a></li>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Safety'><span>Safety</span></a></li>
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<li class='last'><a href='https://2015.igem.org/Team:SPSingapore/Medals'><span>Medals</span></a></li>
 
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         <li><a href = "https://2015.igem.org/Team:SPSingapore/esa"><span>ESA Quorum Sensing</span></a></li>
         <li><a href = "https://2015.igem.org/Team:SPSingapore/Workshop Materials"><span>Workshop Materials</span></a></li>
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         <li><a href = "https://2015.igem.org/Team:SPSingapore/Invasin"><span>Invasin + Listerolysin</span></a></li>
         <li class = 'last'><a href = "https://2015.igem.org/Team:SPSingapore/Interview"><span>Consultations</span></a></li>
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        <li><a href = "https://2015.igem.org/Team:SPSingapore/Anaerobic Promoter"><span>Anaerobic Promoter</span></a></li>
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<li class='last'><a><span style = "background-color:midnightblue"><br>"An expert is someone who knows some of the worst mistakes that can be made in his subject and how to avoid them.<br><br> - Werner Heisenberg</span></a>
 
 
 
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<td colspan=1 style = "box-shadow: 0 0 0; padding:0;border-top:5px white;font-size:15px"><h1>Consultations with Experts</h1></td>
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<td colspan=1 style = "box-shadow: 0 0 0; padding:0;border-top:5px white;font-size:15px"><h1>Anaerobic Response System</h1></td>
 
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Introduction
 
Introduction
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Our project involves engineering E.coli to invade tumour cells in order to deliver drugs to kill the tumour from within. This essentially requires the engineered cells to display pathogenic properties when two conditions localising the engineered cells to the tumour core are present - lack of oxygen and sufficient number of E.coli present (<a href = "#fig1">Figure 1</a>). Please refer to the <a href = "https://2015.igem.org/Team:SPSingapore/Project">Project</a> page for more details on the genes and proteins involved.
 
 
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<figure id = "fig1"><a href = "https://static.igem.org/mediawiki/2015/d/d4/SPSingapore_Interview_Fig1.png" target = "_blank">
 
<img src = "https://static.igem.org/mediawiki/2015/d/d4/SPSingapore_Interview_Fig1.png" width = 500px;></a>
 
<figcaption><b>Figure 1 :</b> Diagram representing the system that the project aims to construct</figcaption>
 
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The two conditions required for expression of the listeriolysin and invasin genes are the two forms of controls exerted on the system. We were concerned that this control might not be tight enough, i.e. the genes may be expressed even when the two conditions are not met. This is usually termed ‘leaky’ expression. For insights on how to address this, as well as other issues elaborated upon below, we consulted two principal investigators, Dr Matthew Chang and Dr Ian Cheong, and respective members of their labs, Adison Wong and Adrian Ng.
 
 
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Design and Control of the Bacterial System
 
 
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A major problem with cancer therapies is the low specificity of many treatment drugs (Chari, 207; Wadia & Dowdy, 2005). Conventional therapies are often administered in a systemic fashion, leading to numerous unwanted off-target effects. To mitigate such issues, there is thus a need for targeted drug delivery systems for anticancer drugs.
Dr Matthew Chang and Dr Ian Cheong are principal investigators at the Centre for Life Sciences (CeLS) in National University of Singapore (NUS), and the Temasek Life Sciences Laboratory (TLL) respectively. Dr Chang’s laboratory deals with synthetic biology of microbial systems while Dr Cheong’s laboratory focuses on finding out novel cancer therapeutics. The former is also programme leader for the NUS Synthetic Biology for Clinical and Technological Innovation programme. While their valuable opinions are not reflected in our current project due to time constraints, we do intend to pass this knowledge on to a future iGEM team.  
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Bacteria have long been considered promising candidates for drug delivery (Patyar et al., 2010). Some strains of bacteria are highly anaerobic, and can only survive in hypoxic environments. As the tumor microenvironment is one of the few hypoxic sites in the human body  (Dachs et al., 1997), anaerobic bacteria will therefore thrive in hypoxic tumour cores and die in oxygenated regions, allowing greater specificity in targeting (Malmgern & Flanigan, 1955; Patyar et al., 2010). Clostridium novyi, an anaerobic bacterium, was found to successfully reduce tumour sizes in phase I clinical trials (Patyar et al., 2010). However,  Clostridium is relatively more difficult to manipulate than other strains of bacteria, making it an unideal choice of a delivery vector.
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Besides strictly anaerobic microbes, there exist other bacteria strains which are facultative anaerobes, the most well-known being Escherichia coli. These strains can survive in both aerobic and anaerobic environments by changing their gene expression programmes accordingly (Salmon, 2013). Thus, we can utilise the natural ability of E. coli to express certain genes under anaerobic conditions to express therapeutic genes or drugs only in the hypoxic core of the tumour.  
 
<br><br>
 
<br><br>
When we asked Dr Chang about controlling leaky expression, he suggested that we could carry out further characterisation of the anaerobic pNirB promoter we intend to use (see our BioBrick part submissions), to see if it responds to any other input.
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However, the tumour core is not the only hypoxic location in the body. For example, the bone marrow (Asosingh et al., 2005) and gut are also hypoxic environments in which the anaerobic expression programme may be activated. As a result, there is a need for more specific control of regulation of the therapeutic drugs or genes.
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Dr Ian Cheong likened promoters to diodes and resistors - diodes only conduct electricity after a threshold voltage (‘all-or-nothing’) whereas resistors conduct electricity incrementally. A resistor-like promoter would continually express the gene at a basal level but increase expression level with more inducer. For instance, in our system, the promoter controlling the effector genes should ideally behave in a diode-like manner. On the other hand, the anaerobic pNirB promoter can be allowed to have some non-anaerobic expression, since a high number of E. coli and hence high AHL concentration is needed before the second switch can be turned on.
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As we were talking, Adison from Chang’s lab suggested that we could rethink our initial two-plasmid system. The original concept was to construct this system on two separate plasmids (<a href = "#fig2">Figure 2</a>). A ‘transcription factor’ plasmid would constitutively express the esaR repressor and express the esaI protein under anaerobic conditions. A ‘effector’ plasmid would contain the esaR-binding box, and express the effector genes (invasin, listeriolysin, drug of choice) when repression is removed.
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<figure id = "fig2"><a href = "https://static.igem.org/mediawiki/2015/5/58/SPSingapore_Interview_Fig2.png" target = "_blank">
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<img src = "https://static.igem.org/mediawiki/2015/5/58/SPSingapore_Interview_Fig2.png" width = 500px;></a>
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<figcaption><b>Figure 2 :</b> Idealised construction of the system on two plasmids</figcaption>
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Adison proposed that we could place our system in one plasmid for easier transfection, as two plasmids with the same backbone may out-compete each other within the same bacterium (<a href ="#fig3">Figure 3[c]</a>). Initially, the two-plasmid system was conceived with the intention that the drug on the effector plasmid might be easily changed and customised for different types of tumours. However, this suggestion does bear consideration, especially as we may want to propose integrating the entire system into the chromosome to reduce likelihood of horizontal gene transfer.
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Concerning Safety
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In view that the effector genes, invasin and listeriolysin, are bacterial virulence factors; and that not many therapeutic bacteria have reached clinical trials, we also consulted with Dr Cheong and Dr Chang about the safety of the system if it were to reach clinical trial. We had identified two key challenges: [1] preventing severe immune response in the short-term, and [2] avoiding horizontal gene transfer with commensal bacteria in the long-term.
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&#9654; Immune Response
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The use of bacteria in therapies is still a controversial strategy, and to date there has not been any FDA-approved bacterial strains for use in disease treatment. This could mainly be due to the concern of eliciting a massive immune response in patients. When injected intravenously, the therapeutic, but foreign, bacteria will be able to travel to all parts of the body causing a systemic wide immune response. Throughout the body, huge amounts of interleukin-2 (IL-2) and tumour necrosis factor-alpha (TNF-α) will be released, which are key mediators of an immune reaction. Following this, the systemic leakage in the vessels will cause blood pressure to dip. These are the signs of an individual experiencing septic shock and if not treated immediately, the extremely low blood pressure can eventually lead to shock and death.
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However such issues can be avoided if the bacteria is injected intratumourally instead. Dr Cheong suggested that it is then important to engineer our therapeutic strain to be extremely antibiotic sensitive so that treatment can be aborted with the use of antibiotics the moment the bacteria invade into other body parts and the patient starts showing signs of fever. Interestingly, Dr Cheong also pointed out that we could put the immune response triggered by our therapeutic bacteria to our advantage by using them as an adjuvant instead. The bacteria, on top of being able to secrete the drug directly in tumour cells, could be used to stimulate the immune response to act against tumour regions, thus enhancing the anti-cancer effects. He supported this with examples of Coley’s toxin and the use of adjuvant chemotherapy to improve survival rate of bladder cancer patients.
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Our mentors, Linda and Stuti, have also suggested that instead of a chemical compound, the drug could be something non-toxic (<a href ="#fig3">Figure 3[a]</a>), such as short hairpin RNA (shRNA), which acts to silence target gene expression via RNA interference (RNAi). This would serve to minimise toxicity to the bacterium host and reduce safety risks when constructing the system.
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&#9654; Horizontal Gene Transfer
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Horizontal gene transfer describes processes by which nearby bacteria transfer genes to each other - the term horizontal refers to the fact that this gene transfer does not occur ‘vertically’ (as in a family tree). Many bacteria species are known to acquire antibiotic-resistance genes via horizontal gene transfer from non-related species, making it a clinical challenge.
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<br><br>
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In our system, we require invasin and listeriolysin for intracellular drug delivery, but these bacterial proteins are also virulence factors. Upon receiving such genes, originally harmless cells/vectors can essentially become pathogens. This raises the potential for horizontal gene transfer to create pathogens in our body, from the normal array of microorganisms the human body naturally hosts. To address this, our interviewees had some suggestions to reduce its likelihood.
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<br><br>
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First, extra-chromosomal elements are easily shared amongst bacteria - the obvious solution is to integrate the system into the chromosome (<a href ="#fig3">Figure 3[d]</a>). Even then, recombination is still a possibility for gene transfer. Subsequently, Adrian from Cheong’s lab suggested that the likelihood for successful chromosomal recombination can be reduced, if we deliberately introduce restriction enzyme sites into the system, either between the genes or within them (<a href ="#fig3">Figure 3[b]</a>). This increases the likelihood of the engineered gene cassette being cleaved when the bacterium vector dies and releases free DNA to the environment - thus reducing the likelihood of other bacteria taking up the engineered genes.  
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Future Work
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Although we were unable to implement most of the suggestions from our interviewees due to time constraints, we have been able to improve upon the design of our system. The ideas are summarised in <a href ="#fig3">Figure 3</a>.
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<figure id = "fig3">
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<a href = "https://static.igem.org/mediawiki/2015/2/27/SPSingapore_Interview_Fig3.png" target = "_blank"><img src = "https://static.igem.org/mediawiki/2015/2/27/SPSingapore_Interview_Fig3.png" width = 500px;></a>
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<figcaption><b>Figure 3 :</b> Improved system design utilising suggestions:
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<br>
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[a] The drug of choice to kill tumour cells should be non-toxic
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<br>
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[b] Restriction enzyme (RE) sites can be incorporated into the construct to reduce the likelihood of successful horizontal gene transfer
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<br>[c] The entire construct could be incorporated into one large plasmid, to avoid possible complication of out-competing plasmids
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<br>
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[d] The entire construct could be integrated into the bacterial chromosome to reduce the likelihood of successful horizontal gene transfer.
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Revision as of 03:45, 19 September 2015


Anaerobic Response System



Introduction
A major problem with cancer therapies is the low specificity of many treatment drugs (Chari, 207; Wadia & Dowdy, 2005). Conventional therapies are often administered in a systemic fashion, leading to numerous unwanted off-target effects. To mitigate such issues, there is thus a need for targeted drug delivery systems for anticancer drugs.

Bacteria have long been considered promising candidates for drug delivery (Patyar et al., 2010). Some strains of bacteria are highly anaerobic, and can only survive in hypoxic environments. As the tumor microenvironment is one of the few hypoxic sites in the human body (Dachs et al., 1997), anaerobic bacteria will therefore thrive in hypoxic tumour cores and die in oxygenated regions, allowing greater specificity in targeting (Malmgern & Flanigan, 1955; Patyar et al., 2010). Clostridium novyi, an anaerobic bacterium, was found to successfully reduce tumour sizes in phase I clinical trials (Patyar et al., 2010). However, Clostridium is relatively more difficult to manipulate than other strains of bacteria, making it an unideal choice of a delivery vector.

Besides strictly anaerobic microbes, there exist other bacteria strains which are facultative anaerobes, the most well-known being Escherichia coli. These strains can survive in both aerobic and anaerobic environments by changing their gene expression programmes accordingly (Salmon, 2013). Thus, we can utilise the natural ability of E. coli to express certain genes under anaerobic conditions to express therapeutic genes or drugs only in the hypoxic core of the tumour.

However, the tumour core is not the only hypoxic location in the body. For example, the bone marrow (Asosingh et al., 2005) and gut are also hypoxic environments in which the anaerobic expression programme may be activated. As a result, there is a need for more specific control of regulation of the therapeutic drugs or genes.