Revision as of 17:15, 31 October 2017

Experiments:Tumor Sensor

Introduction

We incorporated a module into our system that would allow our engineered bacteria to autonomously decide if they are in tumor tissue or not . This decision is taken upon AND-logic integration of two inputs: AHL and lactate (Figure 1). Only if both these chemicals are present, the downstream modules are activated. To achieve such behaviour, we designed a synthetic promoter consisting of operators taken from BBa_K1847007, part of the Lactate sensing system CITATION and the pLux promoter, part of the quorum sensing system. This promoter is regulated by the two proteins LldR and LuxR. LldR binds to the operators O1 and O2, whereby a loop in the DNA is formed that "hides" the sequence in between the operators from regulatory proteins. When lactate is present and binds to LldR, the protein undergoes a conformational change leading to release of the loop. When LuxR binds to AHL, it also undergoes a conformational change which leads to formation of LuxR homo-dimers that bind to the pLux sequence and recruit RNA polymerase whereby transcription is initiated. For a more thorough explanation visit the circuit page .

Figure 1. Depictions of the three designs of the AND-gates we characterized. Design a) is based on the part BBa_K1847007 while designs b) and c) differ in the spacing after O2 and the numbers of O1 and O2, respecitvely. In all cases, only if both inducers, AHL and Lactate, are present, the DNA should be unlooped, which would lead to exposure of the Plux promoter such that the dimerized LuxR can activate expression of downstream genes.

Initial System Design

The precise genetic design of our synthetic hybrid promoter was inspired by the work of the ETH iGEM team 2015. Based on their synthetic lactate-responsive promoter we came up with the idea to introduce pLux at the place of their constitutive promoter. Considering potential steric requirements of LuxR, the regulator of pLux, we further suspected spacing between pLux and O2 to be of importance. Thus, we designed another version with increased spacing. Additionally, we hypothesized that by including each operator site twice would result in a stronger effect of LldR.

Before we started any designing of regulators, cloning or experimentation on the tumor sensor module, we sat together with our modellers to find key parameters relevant for design and experimentation.

KEY QUESTIONS

Based on previous work done on quorum sensing: how strongly should LuxR and LuxI be expressed?
Quick answer: Each 10 times stronger than the ones characterized here.
Similarly, what expression levels of LldP/LldR should be achieved in order to get enough sensitivity to differentiate tumor and non-tumor tissue?
Quick answer: ...
At what density of the colony under experimental conditions should the quorum sensing system be activated?
Quick answer: At an optical density (OD) of 0.05. The population density in the colonized layer in tumors would translate to an OD of about 60. Contrary to in vivo conditions though, in our experimental setup there would be no diffusion of AHL out of the system, amounting to an "overestimation" of the population density. Therefore, the tipping point of quorum sensing should be at such low ODs.

Overview of the Experiments

To build and characterize an AND-gate that would allow to differentiate between healthy and tumor tissue, we ran a sequence of experiments:

We transformed E. Coli Nissle with plasmids containing only the quorum sensing system and let these colonies grow to different densities and evaluated their response. This way, we aimed to find the "trigger point" of the quorum sensing part of the tumor sensing module. This data could also be used by the modelleres to infer important paramters of the system and thus guide further design.
We evaluated the response of our AND-gate designs to varying amounts of lactate and AHL. Based on this data we aimed to evaluate functionality of the rationally designed hybrid promoters and determine the design most suitable to our system's needs.
Finally, we transformed E. Coli TOP10 with plasmids containing the whole tumor sensor system and evaluated the how the cultures behave over time under conditions corresponding to healthy and tumorous tissue. This way, we aimed at confirming the findings of the previous experiment and show that our system behaves as required for an autonomous interpretation of environmental signal.

To read more about each of these experiments, click on the buttons below. For a detailed protocol describing each experiment, visit Protocols.

Quorum Sensing End-Point Characterization

OBJECTIVE
Determine the population density at which the quorum system gets activated and provide the modellers with data to infer a_LuxI, the production rate of LuxI.

PROCEDURE
We transformed E. coli Nissle with a regulator and an actuator plasmid (see figure 2), coding for constitutive expression of LuxR and Plux, sfGFP, mCherry and LuxI respectively (Figure 2).

Figure 2. Depictions of the cargos of the two transformed plasmids. One codes for the regulator LuxR under the consitutive Anderson promoter J23100. The other plasmid contains Plux which responds to dimerized LuxR by activating transcription of the encoded sfGFP, mCherry and LuxI.

Subsequently, we let these colonies grow to different final population densities. This was achieved by varying glucose concentrations in a defined medium. [1] Population density was assessed by measuring absorbance at 600 nm wavelength. Fluorescence emitted by sfGFP and mCherry served as a read-out of the level of activation. A detailed protocol is available in Protocols.

RESULTS

Figure 3. A) Proof of concept that final population densities can be modulated with the amount of glucose in a defined medium. B) GFP fluorescense per A600 in response to population density. Colonies were grown over night in media with varying glucose concentrations that lead to different final population denisities. With increasing absorbances at 600 nm, increasing fluorescence levels are observed.

CONCLUSION

We can modulate the density a bacterial population reaches in defined medium by varying the amount of glucose.
The quorum sensing system shows a response to increasing population densities.
The steep increase in fluorescence between absorbance 0.4 and 0.5 indicates the threshold for activation of the quorum sensing system to be at around 0.4. As a rule of thumb, we established that OD values are around 4 times higher than A600 values (data not shown) for absorbances around between 0.1 and 0.6 for the same sample. Thus, to fulfill the criterium given to us by the modellers (e.g. activation at an OD of 0.05) further tuning of the system is needed.

AND-gate without Quorum Sensing

OBJECTIVE
Determine the dose-response behaviour of our synthetic AND gate to the two inducer AHL and lactate. In this experiment we wanted to assess whether our designs would be capable to distinguish healthy and tumor tissue based on lactate and expected AHL concentrations.

PROCEDURE
Two plasmids required for the AND-gate were transformed into E. coli Top 10 (Figure 4). Exponential-phase cultures were induced in microtiter plates under combinations of 8 different AHL and 8 different L-lactate concentrations and measured after 5.5 hours growth in the palte. A detailed protocol is available in Protocols.

Figure 4. Schematic depiction of the two plasmids that were transformed for this experiment. One codes for constitutive expression of the regulators of our synthetic hybrided promoters, LldR/LldP and LuxR. The actuator plasmid consists of the AND-gate promoter as well as the fluorescent reporter sfGFP.

RESULTS
All our synthetic promoters react to increasing inducer levels by increasing expression of the encoded gene. Hence, the highest level of activation coincides with the highest amounts of inducers. No activation is observed at low and intermediary concentrations of inducers and only in regimes with high amounts of inducer there is an increase in expression levels. This behaviour is consistent with our expectations.

Figure 5. Dose-respone of the different AND-gates to lactate and AHL. Shown are geometric means of two replicates of fold changes to the uninduced case. Note the strongly increased expression in regimes of highly concentrated inducers vs. the low expression in low-concentration regimes.

Design a shows a 20-fold increase at the high/high regime over the low/low regimes. In case lactate is highly concentrated and AHL is absent, there is already some activation of around 9-fold. Similarly, highly concentrted AHL alone leads to an increase in expression of around 4-fold.
With a GFP-expression level 48-fold higher in presence of both inducers at high levels than in absence of both inducers, design b shows the strongest response to the inducers. Similar to design a, there is some activation even if only one of the two inducer is present in high amounts.
Design c shows the smallest response to high inducer levels with activation of around 16-fold. The observation of activation in presence of high levels of only one inducer is made for this design as well.

CONCLUSIONS

Our synthetic AND-gate promoter responds to both inputs lactate and AHL. Thus, it enables the engineered bacteria to sense the environment with regard to the inducers we chose.
Indepently of the amount of the cognate inducer, both lactate and AHL alone at high concentrations lead to increased expression levels.
While characterizing the MRI Imaging Module, a dose-response curve of the pLux promoter to AHL was obtained. There, it was found that the threshold for induction is around 10^(-7) M AHL. Here, this value lies around 10^-(5) M AHL. Thus, we came to realize that we cannot compare the behaviour of pLux alone to that of pLux in the hybrid promoter context, we dropped the line of engineering where we aimed at decreasing sensitivity of the quorum sensing system independent of our AND-gate. We hypothesize that this decrease in sensitivity is caused by reduced accessability of LuxR to the pLux promoter. Indeed, the modelling team was able to reproduce this effect. LINK!
Considering that in healthy tissue lactate levels of around 1 mM were found while these values were found to be at around 5 mM in tumor tissue CITATION, we see that there is a large difference in activation between "healthy" lactate levels vs. "tumor" lactate levels. For all promoter designs and over all AHL concentrations, activity is increased consistently around 3 to 5 times from "healthy" to "tumor" lactate levels.
Considering further that AHL levels in non-tumorous tissue would be low in the first days after administration of CATE to zero after 3-4 days CITATION, we see that also for AHL there is a marked difference in activation at "healthy vs. "tumor" concentrations.
Based on this data we conclude that our hybrid promoter allows CATE to distinguish lacatate and AHL levels of healthy tissue to that of tumor tissue.

AND-gate with Quorum Sensing

OBJECTIVE
Verify the findings of the AND-gate characterization without quorum sensing with strains of E. Coli that contain additionally to the AND-gate also LuxI, the enzyme that catalzyes AHL production.

PROCEDURE
Two plasmids required for the AND-gate were transformed into E. coli Top 10 (Figure 6). Cultures were grown over night in deep-well plates in media with varying lactate concentrations. The measurements of population density and GFP fluorescence were taken after ~16 hours on a plate reader. A detailed protocol is available under Protocols.

Figure 6. Schematic depiction of the two plasmids that were transformed for this experiment. Lactate is provided to the system in this experiment, AHL is synthesized by the cells themselves.

RESULTS
The data is very noisy and it’s hard to make general statements about this systems behaviour. Despite this, a clear trend is visible for GFP to be higher expressed under lactate concentrations similar to tumor tissue than under those resembling healthy tissue or no lactate at all. With increasing population densities this effect becomes less pronounced (Figure 7).

Figure 7. Fluorescence normalized to population density vs. population density. Blue circles correspond to media lacking lactate, green to media containing 1 mM lactate, and red to 5 mM lactate. Circle styles correspond to three different biological replicates. It becomes apparent that with higher densities comes higher activation and that for lower population densities, lactate has a positive influence on GFP expression levels.