Team:KULeuven/Project

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Project brainstorm

Favourite previous iGEM projects


Maarten Breckpot


Nathalie Busschaert

  • [http://parts.mit.edu/igem07/index.php/Imperial/Infector_Detector/Introduction Infector detector] - Imperial College 2007
  • [http://parts.mit.edu/igem07/index.php/Edinburgh Self-flavouring yoghurt] - Edinburgh 2007
  • [http://parts.mit.edu/igem07/index.php/Paris Synthetic Multicellular Bacterium] - Paris 2007


Jonas Demeulemeester

  • [http://parts.mit.edu/igem07/index.php/Ljubljana Virotrap Ljubljana 2007]
  • [http://parts.mit.edu/igem07/index.php/Princeton RNAi enhanced logic circuit Princeton 2007]
  • Other nice parts/devices:
    • Caltech: Riboswitch design for targeted cell death/molecular sensor
    • Cambridge: Inducible bigger pore protein for E.coli
    • Harvard: Quorum-sensing & targeting!
    • Melbourne: Red/blue light responsive system through chimeric photoreceptors-kinases
    • Peking U: λ-based bistable switch = very powerful
    • UCSF: compartmentalization! Rewired MAPK cascade signaling through scaffolds ≅ circuit board


Andim Doldurucu


Jan Mertens

  • [http://parts.mit.edu/igem07/index.php/Ljubljana Virotrap Ljubljana 2007]
  • [http://parts.mit.edu/igem07/index.php/Berkeley_UC Bactoblood]


Benjamien Moeyaert

  • [http://openwetware.org/wiki/IGEM:Harvard/2006/DNA_nanostructures Harvard 20006: nanostructured DNA containers]
  • [http://parts.mit.edu/igem07/index.php/Berkeley_UC Bactoblood]


Stefanie Roberfroid

  • [http://parts.mit.edu/igem07/index.php/Cambridge Bacteria Online]
  • [http://parts.mit.edu/igem07/index.php/Berkeley_UC Bactoblood]
  • [http://parts.mit.edu/igem07/index.php/Princeton RNAi enhanced logic circuit]
  • some other nice ideas
    • [http://parts.mit.edu/igem07/index.php/Edinburgh Self-flavouring yoghurt]
    • Detection of metals: [http://parts.mit.edu/igem07/index.php/Brown Lead], [http://parts.mit.edu/igem07/index.php/Saint_Petersburg Copper]


Hanne Tytgat

  • [http://parts.mit.edu/igem07/index.php/Berkeley_UC Bactoblood]
  • [http://parts.mit.edu/igem07/index.php/MIT Sensing & removing Hg ions - MIT 2007]
  • [http://parts.mit.edu/igem07/index.php/Imperial/Infector_Detector/Introduction Infector detector]


Elke Van Assche

  • [http://parts.mit.edu/wiki/index.php/MIT_2006 Eau d'E.coli MIT 2006]
  • [http://parts.mit.edu/igem07/index.php/Berkeley_UC Bactoblood Berkeley UC 2007]
  • [http://parts.mit.edu/igem07/index.php/Princeton RNAi enhanced logic circuit Princeton 2007]


Nick Van Damme

  • [http://parts.mit.edu/igem07/index.php/Davidson_Missouri_W Bacterial Computer]

--> idea: solve a nice mathematical problem

  • several electronical/biological components to build an entire complex combinational logic system
    • [http://parts.mit.edu/igem07/index.php/USTC Extensible Logic Circuit in Bacteria]: both components and linking
    • [http://parts.mit.edu/igem07/index.php/Valencia Comparator]
    • [http://parts.mit.edu/igem07/index.php/Bologna Schmitt trigger]

--> idea: build an integrator to solve your own ODE's, also build a differentiator to make a PID-controller


Antoine Vandermeersch

  • [http://parts2.mit.edu/wiki/index.php/University_of_Texas_2006 Texas 2006: Edge Detector]
  • [http://parts.mit.edu/igem07/index.php/Rice/Project_B:_Quorumtaxis Rice 2007: Quorumtaxis]
  • [http://parts.mit.edu/igem07/index.php/Berkeley_LBL Berkeley LBL 2007: Solar Bacter]


Dries Vercruysse


Sigrid De Keersmaecker

  • [http://parts.mit.edu/igem07/index.php/MIT Sensing & removing Hg ions - MIT 2007]
  • [http://parts.mit.edu/igem07/index.php/Edinburgh Self-flavouring yoghurt - Edinburgh 2007]
  • [http://parts.mit.edu/igem07/index.php/Missouri_Miners Biological Timer - Missouri Miners 2007]
  • [http://parts.mit.edu/igem07/index.php/Ljubljana Virotrap - Ljubljana 2007]
  • [http://parts.mit.edu/igem07/index.php/Taipei/Taipei GlucOperon - Taipei 2007]
  • [http://parts.mit.edu/igem07/index.php/Berkeley_LBL Solar Bacter - Berkeley_LBL 2007]
  • [http://parts.mit.edu/igem07/index.php/Berkeley_UC Bactoblood - Berkeley_UC 2007]

iGEM judging tracks

  • Foundational Research - basic science and engineering research
  • Information Processing - genetically encoded control, logic, and memory
  • Energy - biological fuels, feedstocks, and other energy projects
  • Environment- sensing bioremediation of environmental state
  • Health & Medicine - applied projects with the goal of directly improving the human condition

Other

[http://openwetware.org/wiki/IGEM:Idea_exchange Idea exchange - iGEM ideas posted by other teams]

Ideas for our project

A first idea: cancer treatment with genetically modified blood cells

As cancer cells need a lot of energy to replicate themselves, they should be well provided with blood. Therefore, blood cells could be the right choice for in situ treatment of cancer. First, we should immobilize these blood cells on the cancer cells. Subsequently, these blood cells should secrete specific agents that reduce the activity of the cancer cells. (These 2 steps may come in handy if we want to split up in 2 subgroups)

Notes

  • Sounds like a great idea! [http://en.wikipedia.org/wiki/Avastin Anti-angiogenic therapy] is one of the big hopes for anti-tumor treatments. But let's keep in mind that angiogenesis (the formation of blood vessels) is only a late hallmark of tumors [http://www.google.be/url?sa=t&ct=res&cd=1&url=http%3A%2F%2Fwww.weizmann.ac.il%2Fhome%2Ffedomany%2FBioinfo05%2Flecture6_Hanahan.pdf&ei=-7E2SLbLGJCE1wblseHQDQ&usg=AFQjCNHirXaVMmdQNGl-72bk5jRva4106Q&sig2=L18rRG56VaP9wIB_mAENpA (more about these hallmarks of cancer -PDF)]. It is however a significant barrier to break through if the tumor has to grow past a certain (very limited) size. So this would be more like a therapy for later-stage malignancies, which would also be great because it's often the metastasis (the spreading of) of the tumor that is causing the more visible effects of the cancer. (pain, deterioration, ... and eventually, if untreated death). - Jonas 12:09, 23 May 2008 (UTC)
  • Anyhow, if we proceed with this idea, it will be a challenge to get everything ready and produced in the erythrocyte (red blood cell) before it loses it's nucleus and thus also the ability to initiate de novo transcription. And to keep all this machinery silent in non-docked erythrocytes. I'm liking this challenge though. Besides this has an upside as well as I feel that consequences would be less severe in this non-cell if things go awry in the system. :) - Jonas 17:30, 23 May 2008 (UTC)
  • I just thought of something that might be quite critical. If I recall correctly, there are 3 main ways in which tumors acquire blood supply.
  1. The first one is through a recapitulation of embryonic development. This is the recruitment of vascular endothelial precursors or the activation of local endothelium via factors like VEGF (angiogenic sprouting or intussusceptive growth). In this case, the 'vessels' of the tumor blood supply are lined mostly with endothelial cells which are actually NOT malignant, but are kind of working together with the tumor cells.
  2. A successful cancer metastasis (a secondary tumor, derived from the original) will co-opt blood vessels and these will thus also be lined mostly with endothelium cells.
  3. The third way to achieve blood supply is through vasculogenic mimicry, where the tumor cells actually DO line the bloodstream and mimic the normal vascular endothelium. Here tumor biomarkers should be directly displayed to the passing erythrocytes and would thus be potential targets for use in this approach.
OK, now for my point. In all these cases the vessels are highly abnormal, both structurally and functionally. They've got many holes, inhomogeneous bloodflow, are leaky, ... so it's very likely there will be exposed markers we can focus on but this will probably not always be the case. But anyhow, I'm really liking this idea! - Jonas 14:17, 23 May 2008 (UTC)
  • There will be a lot of challenges. Some things that popped in my head: 1)What is the progenitorcell we're going to work with. When you use stemcells, you have to differentiate them in vitro into red blood cells which is pretty delicate matter. 2)finding the right markers for the recognition that are not expressed on normal cells. 3) developing an assay that proves that it works. Whith tis idea there are a lot of factors that have to be taken in account and the question is if we will get a positive result in 3 months time. There's a lot of ongoing research and a lot of things ar not yet known. But I also like the idea, next year I'm going to do my thesis about lymphangiogenesis so I'm very interested in the subject :)- Jan
  • On the biomarker issue. There's a lot of this kind of proteomics research going on at the Biology faculty/GHB. I hope we could pick up some molecules there? Because starting our own search for these and getting results in 3 months time would be quite hopeless indeed - Jonas 23:46, 23 May 2008 (UTC)
  • I agree that working with RBC will be quite a challenge. But maybe we can use bacteria with the right proteins, just to proof the principle. If it works, another team (next year?) or research group can then try to apply this principle on RBC. Anyhow, I also really like this project. --BNathalie 16:18, 24 May 2008 (UTC)
  • We could overcome the differentiation problem if we work with a mouse model for example. We harvest (or get them from someone) CD34+ hematopoietic progenitor cells (or other progenitors, I don't know), transfect these with our constructs + maybe an extra marker like green fluorescent protein (GFP) and then reintroduce these cells into the mouse. Differentiation should proceed normally then and we could harvest the modified and differentiated red blood cells (RBCs) by FACS analysis or something similar. The problem is that I've got no idea how long a procedure like this could take and we should be sure that our constructs work properly before trying this. We could also attempt myeloablative treatment on the mouse before reintroducing the transfected cells, this would make reharvesting a lot easier but once again, no idea how long this takes ... On the other hand, if we could harvest the modified RBCs, an in vitro assay should be quite feasible. - Jonas 22:06, 24 May 2008 (UTC)
  • I've been thinking about the agent we have to deliver in order to kill the cancerous cells. We could deliver Reactive Oxygen Species (ROS) like hydroxyl radicals, superoxide, hydrogen peroxide or singlet oxygen to the tumor. This could potentially be very hazardous or lethal to the tumor cells since they often have defective DNA repair machinery and would thus be unable to cope with this amount of damaging. The erythrocyte vessel we target to the tumors is extremely well fitted to do this since it's packed with iron that could potentially catalyse the production of a lot of these ROS via the [http://www.lenntech.com/Fenton-reaction.htm Fenton reaction] etc. So all that should happen after the erythrocyte docks to the cancerous cells would be to destroy some hemoglobin, set some iron free in the red blood cell and let ROS be created locally! - Jonas 09:00, 24 May 2008 (UTC)
  • One last thing. The entire erythrocyte metabolism has been [http://www.tbiomed.com/content/2/1/18 simulated] in silico (including links to hemoglobin). So this project could also provide enough entertainment for the more modeling-oriented amongst us :) - Jonas 23:12, 25 May 2008 (UTC)

A second idea: bacteria clean virusses in animals

This is an improvement of the idea of Ljubljana: we cannot reprogram the immune system, but we can reprogram bacteria. So, what we could do is make bacteria produce viral receptors (challenge 1) which are modified so that when a virus attaches to them, a restriction enzyme is transcribed (challenge 2). This RE degrades the viral DNA and the bacterial DNA, thus killing the bacterium. This way, the bacteria clean all virusses from the body. When this is established, we can induce a suicide signal for the bacteria (challenge 3). Big problems:

  • Is it possible to make a eukaryotic virus attack a prokaryote (also a fundamental question)?
  • Immunogenicity bacterium (cf. Bactoblood)! Bmoeyaert


  • I'm probably risking to get banned for nagging because of this. :P I think the tricky part would be the preferential docking of the viruses on the bacteria if you've got about 10^14 of your own cells in your body. Even if only a small subset of these would be targets for the virus, I believe the ratio of bacteria to host cells would be quite low unless you allow a very large 'bacterial infection'. This problem might be overcome if the viral receptor density is way higher on the bacteria. - Jonas 17:52, 23 May 2008 (UTC)
  • Cool stuff though, the opposite system exists. A bacterial infection could be treated by administering the specific bacteriophages, here the system can also co-evolve. Problem is that you have to know the bacterial strain of the infection in order to administer the correct phage, and this can take a while. - Jonas 17:52, 23 May 2008 (UTC)
  • It's an appealing concept. An eukarotic virus only has to cross the celmembrane to get its content into the human cell. When we would use E.coli, the virus would have to get first through the outermembrane, then through the peptidoglycane and then through the innermembrane. So how does it get it in the cytoplasm? But maybe this is not necessary and is it sufficient to let the virus cross the outermembrane and come in the periplasm. If this induces the cell to do apoptosis en kill itself, including the virus, we've got a nice system. But like Jonas said, there will always be virusparticles that infect human cells, wich are in the majority. But still, it would be quite an accomplishment to get an eukariotic virus to infect a bacterium.-Jan

A third idea: Bacteria that control the amount of drugs

It's known that the effect of drugs on a human being is very dependent on the metabolism of that person. There are extensive metabolizers, people who have a normal response to a certain drug. Intermediate metabolizers show a low response and in poor metabolizers there's very little effect. Poor metabolizers need a higher amount of drugs to respond, where ultra fast metabolizers need a lower dose. These differences in the drugmetabolism in different people is a big concern, because a wrong dose can have severe consequences. There's a need for patient-focussed therapy. If we want to know which type of metabolizer a person is, we have to know his genotype. This is a very expensive and time-consuming procedure. Wouldn't it be nice to develop a two bacteria-system that can replace genotyping? I' m thinking of two bacteria that live together in the intestine. The first bacteria has a sensor function. It has to monitor if the amount of the drug that is present in the intestine, is efficient. This bacteria has to signal his observations to the second bacteria. This second bacteria is the drug-producer. Like some probiotics, that are already on the market, it produces the drug at the location where it's needed. The amount of drug it produces would be controlled by the other bacteria. In case the amount of treatment is enough, the first sensor-bacteria represses the second one. If the drug level drops again, the sensor-bacteria should re-activate the drug-producing one. In that way there's a feedback loop between the two bacterias and one can control the amount of treatment that's needed. --Hanne 19:27, 23 May 2008 (UTC)

  • I don't think you necissarily need a 2 bacterial strain system and can also do it with one bacterial strain that has sensor- and drugproducer function. When it monitors the amount of drugs it can autoinduce itself to produce the drug and repress itself when it's enough. like the idea and think it's possible to do this in 3 months. It's also an idea in which I see our different skills can be integrated (the engineers can do modelling of pharmacokinetics for example), In the first 2 ideas that's maybe more difficult -Jan
  • I would streamline the idea further:
    • Use a single probiotic bacteria (lots of available expertise on probiotics in the team)
    • Use a peptide or protein drug - probably a lot easier than synthetisizing a small molecule
    • As probiotic bacteria live in the gut, peptide or protein drug could probably enter the blood stream
    • Make a sensor for a signal that indicates the reaction to the treatment
    • I was thinking about Crohn's disease (because it happens in the gut). Produce a peptide such as vasoactive intestinal peptide (potential treatment for Crohn). Sense the inflammatory response present in the gut. If high inflammation, increase drug production - up to some maximum dosage to avoid overdosing. Do not respond too fast to avoid overdosing.
    • Crohn's expertise available in Leuven (P. Rutgeerts, S. Vermeiren) --Yves
  • I also like this idea. However, you can't really control how long the bacteria stay inside your gut. So I think this is a system that is best used for chronic conditions (like Crohn's disease) that require continuous treatment. I like the example of Crohn's disease, because you can build in a good control devise to avoid overdosing. In this system, we need a bacteria that produces a drug only when: a) there is a low concentration of the drug inside the gut, and b) when the gut is inflamed. Practically, this means a receptor that will stop the production of the drug upon binding to the drug. I don't know how to sense inflammation though. --BNathalie 16:35, 24 May 2008 (UTC)
  • I was indeed thinking of applications for chronic disease. --Y
  • In the case of Crohn's, I think it would be quite doable to sense inflammation as there are many molecules typical of this process. We would have to look up which ones though. --Y
  • An additional advantage is that Crohn's disease is characterized by local inflammation, so that the system would probably produce more drug exactly where it is needed most. --Yves
  • I also like this idea. Like Jan says it's a project were we are going to need all our different skills. Maybe this is more interesting for the engineers among us because it needs a lot of modeling. --stefanie
  • As an engineer this also seems the most challenging proposal. To regulate the proportion of drugs it seems that we are going to need a PID-controller (proportional with the amount already available, integrating to keep the level steady and differentiating to avoid responding too fast). It would be very challenging if we could also achieve this kind of controlling system in the bacteria. --Nick
  • Genetically modified Lactococcus lactis bacteria constitutively expressing Interleukin-10 (anti-inflammatory) are [http://www.ncbi.nlm.nih.gov/pubmed/16716759?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum already in stage I clinical trials] for the treatment of Crohn's disease. The dosage regulation by sensing could be a very nice addition to a system like this. I don't know however to what degree Crohn's disease is temporally variable and thus might benefit from such a system. - Jonas 23:28, 25 May 2008 (UTC)
  • I think you see it somewhat wrong. It's about sensing what amount of drugs a certain patient needs. So there is a variable, not only in one patient, but also between different patients! It's about sensing how much every person needs. I think the idea of implementing this system for the treatment of Crohn's disease is really interesting. It's true that Lactobacillus lactis already delivers the drugs at the right spot in the body, but the control mechanism isn't there yet. So I think we could make an important improvement to this approach. This system can than serve as a model for treating other diseases. --Hanne 09:13, 26 May 2008 (UTC)
  • The reference signal for the PID would simply be the local inflammation, but does this mean the bacteria would extract no information about the specific metabolism of the host (person)? If it would, the PID-controller could be optimised for every person by means of self-tuning (retrieving optimal parameters that characterise the PID-controller behaviour and determines it stability). Anyway, I like this idea a lot. EDIT: just saw Hanne's post, this is indeed what I ment --Avdmeers
  • Ideally, the dosage would be patient specific and variable in space and time. In space, because the disease is not uniform across the intestine (some regions are in a better condition while others are worse). But I guess that because the mixing and diffusion that happens in a fluid environment, it is hard to control for production at a very specific spot on the intestine, except if the bacteria would stick to the intestine wall itself (might be possible with the right bacteria). However, patient specific dosage and time variability would be a very interesting advantage as not all patients have the same severity of the disease and as the disease progresses with up-and-downs ("The disease is characterized by active periods, known as flare-ups, followed by periods of remission, during which symptoms diminish or disappear altogether. Its cause is not known." - ehealthmd.com). Basically, the drug would be self-dosing. --Y
  • The project does indeed bring together the interests of many people: a realistic medical application, work on bacteria that looks doable, and a tractable modeling problem based on well-known engineering principles (control engineering). --Y
  • As a security mechanism, I guess that the bacteria are simply sensitive to antibiotics and thus a course of antibiotics is sufficient to stop the treatment altogether. --Y
  • Possible extension for later: sensing adverse reaction. Some patients might respond badly to the treatment. We could have a system that senses physiological distress from the patient and then shuts down the drug production. This could be faster than giving antibiotics. Something like that might also work for patients who metabolize the drug differently (slower and faster) and for whom baseline level (i.e., for the same degree of inflammation) of the drug need to be lower or higher. --Yves
  • People in Leuven (Gastroenterology lab) are collaborating on the studies on IL-10-producing lactobacillus. This product is being developed by a spin-off of the Flanders Institute for Biotechnology (VIB) called Actogenix (www.actogenix.com) --Y
  • You could sense several cytokines, such as TNF-alpha, interleukin-1, interleukin-6 as a measure of disease status. I guess for a cytokine, you could use a corresponding cytokine receptor as sensing device. --Y
  • An important issue is whether those disease-marker proteins are measurable in the gut. I would assume so since they are probably produced at the inflammation site (but not sure about that). --Y
  • Other important markers are fecal calprotectin (so most probably present in the gut) and C-reactive protein. --Y
  • Like Yves, I was also thinking about what we could sense while remaining on the luminal side of the gut. The localisation of the cytokines might not be a problem since the surface of the gut lumen is severely damaged in the patient and even blood can be exposed. Since the inverse works; the IL-10 can get in, the others should be able to get out I presume. I don't know how long these proteins last in the gut though (because f degradation by other bacteria/our own proteases) and thus how long they are able to constitute a valid signal. But once again the Interleukin-10 in clinical trials seems to last long enough, so this might not be a problem either. - Jonas 16:09, 26 May 2008 (UTC)
  • If we go through with this project, I feel like we should keep modularity of the system in mind. This could make the introduction of other sensors or other output molecules a lot easier if knowledge about the disease progresses. So we would basically be creating a platform for Crohn's or other inflammatory bowel diseases on which anyone could further build, switching inputs, outputs and stuff. And if we've got spare time during the summer we could implement extra sensors or switching output molecules ourselves. - Jonas 16:09, 26 May 2008 (UTC)
  • PS: maybe Eicosanoids or other non-protein inflammatory molecules could also be used to detect the inflammation. These wouldn't be bothered by proteases and can travel through cell membranes so they should definitely be present in the gut (if they are produced in Crohn's) and they can be easily picked up by nuclear hormone receptors. - Jonas 16:14, 26 May 2008 (UTC)
  • Both measuring cytokines and eicosanoids seem viable options (see http://gut.bmj.com/cgi/content/full/46/4/487 with TNF-alpha and IL1-beta (and IFN-gamma) as cytokines, and Thromboxane B2 and prostaglandin E2 as eicosanoids). So it would be a question of what is easier for the experimental work. My impression though is that many eicosanoids are detected by transmembrane receptors rather than nuclear receptors. --Y
  • Most eicosanoids do indeed bind to GPCR transmembrane receptors but some can also bind to PPAR subfamily nuclear receptors, these form heterodimers with the retinoic X receptors and can immediately induce gene expression. With a GPCR we'd have to construct a longer signal transduction cascade in the bug (which could allow additional regulation). Nuclear or membrane, it shouldn't make a big difference for eicosanoids since they can get through the membrane anyhow. For the cytokines we only have transmembrane receptors which won't work/be accessible in bacteria I think. - Jonas 22:46, 26 May 2008 (UTC)
  • For a proof of concept, we would need to be able to set up such a system in vitro. The drug production could be "simulated" by replacing it by the production of GFP. We would then need a system for controling the level of the signaling protein (e.g., TNF-alpha cytokine). We can easily increase the level of the signaling protein by spiking in a fixed amount of it. But how do we decrease it? We cannot really have a model of the response of the gut to the drug. Maybe we could precipitate the signaling protein with an antibody? And how do we measure the concentration? By fluorescently labeling the signaling protein? --Y
  • Another setup (probably much easier) could be to
    1. Grow the bacteria on a dish
    2. Remove them from the original medium
    3. Put them in a medium with a high concentration of signaling protein (i.e., TNF-alpha)
    4. Observe that production of GFP SLOWLY ramps up (maybe up to some maximum threshold to avoid overdosing)
    5. Put the bacteria back into a medium with a low or zero concentration of signaling protein
    6. Observe that GFP production is turned off slowly --Y
  • We still have to face the problem of what organism to use and how it will sense what we want it to sense. For example L. lactis is gram-positive with a big layer of peptidoglycan shielding off it's membrane surface. So how will the signaling molecule be sensed? The TNF-alpa trimer is quite big. If we use a gram-negative like E. coli we will still have to have our signal transduced through the periplasm. This might prove to be quite tricky - Jonas 17:19, 26 May 2008 (UTC)

Our project

Abstract

Our project details

Part 2

The Experiments

Part 3

Results

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