Difference between revisions of "Team:Fudan/Part Collection"

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<div class="block main-text sub-title  dark-blue">
 
<div class="block main-text sub-title  dark-blue">
   <h class="sup-title dark-blue">SwordS</br></h>
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   <h class="sup-title dark-blue">Part Collection</h>
  <h class="sub-title dark-blue">enables antigen density dependent tri-response for therapeutic applications</h>
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<h2> </h2>
 
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<div class="block main-text main-text">
 
<div class="block main-text main-text">
  <h class="highlight-title dark-blue"></br></br>Abstract</h>
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   <p>As a team focusing on real-world problem, we found it is hard to obtain sufficient mammalian Biobricks on the Registry of Standard Biological Parts comparing to the convenience for project in bacteria. In synthetic biology, one central route is to construct a controllable biological network, and electing suitable transcription factor and corresponding promoter is vital.  
   <p></br>Antigen density on tumor cells’ surface is heterogeneous. Current cellular immunotherapy only targets cells with high expression of specific tumor antigen. While this approach can improve the precision of recognition, it loses the opportunity to strategically treat tumor cells with different surface antigen densities. We are the first to propose a cellular immunotherapy platform, SwordS (SynNotch-Stripe system), that is capable of generating non-monotonic therapeutic responses to one tumor antigen with different surface densities. We demonstrated our concept with the following experiments. In combining a SynNotch module, which can recognize the antigen, and a Stripe module, which can sort intracellular signal, our engineered cells could generate antigen density dependent tri-response against the target cells with different densities of surface GFP, as well as membrane GPC3 (the tumor antigen of hepatocellular carcinoma). Both experimental data and mathematical simulation show that our platform not only reduces the on-target/off-tumor effects of the original SynNotch system, but also provides a combinational therapeutic solution to treat tumor at various states. We believe that SwordS is a promising platform for the next generation cellular immunotherapy. </br></br>
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<p>
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The best way to predict the future is to invent it. As we couldn’t find Biobricks that were completely satisfying to us, we just invent it.  
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<p>
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For this year’s iGEM competition, we present an approach to design customized mammalian synthetic transcription factor (SynTF) - synthetic promoter (SynPro) pairs. This set is a powerful toolbox to construct customized and orthogonal transcriptional network.
 
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<div class="block main-text main-text">
 
<div class="block main-text main-text">
   <h class="highlight-title dark-blue" id="Antigen"></br></br>SwordS</br>Antigen density heterogeneity and limited treatment, two obstacles in improving therapeutic effect and applicability of immunotherapy</h>
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   <h class="highlight-title dark-blue" id="Antigen"></br></br>How to design SynTF-SynPro</h><h2> </h2>
  <h class="bold-text"></br></br>Target antigen density heterogeneity</h>
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   <p>SynTFs enable binding to user-specified DNA sequences, response element (REs), on SynPros then silencing or activating their transcription. The SynTFs we designed were in an unified style containing three core domains from N-terminal to C-terminal: DNA binding domain (DBD), nuclear location sequence (NLS), transcription regulating domain. We chose (G4S) as linker to be added between DBD and SV40 NLS for region flexibility. We could choose KRAB or VP64 as transcription regulating domain to construct silencing- or activating-form SynTFs (SynTF(S)s and SynTF(A)s). The structures of their corresponding silencing- or activating-form SynPros (SynPro(S)s and SynPro(A)s) were pSV40-N*RE or N*RE-minCMV.
   <p>The expression of the antigen on individual cells within a given tumor is different or heterogeneous. A solid tumor mass consists of numerous tumor cells. In these tumor cells, some may express relatively less tumor antigens, others may express relatively more tumor antigens. Meanwhile, a given tumor antigen is not only expressed on malignant cells, but may also be expressed on normal cells at a low level <font color="#004a84">(Figure 1A)</font>. Thus, normal cells expressing low level of tumor antigens subsequently should not be targeted, otherwise would casuse complications. Carefully control the on-target/off-tumor effect is critical for the success of immunotherapy. <font color="#004a84">(Figure 1B)</font> </br></br></br>
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<img src="https://static.igem.org/mediawiki/2017/c/ca/T--Fudan--PCFigure.jpg">
 
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   <p>The critical step to find optional SynTF group is to find enough differently specific and orthogonal DBDs. We applied two approaches to achieve this. Firstly, we widely investigated those commonly used DBD originating from different species. Secondly, we devised a platform based on artificial zinc-finger (ZF). For the first idea, we chose Gal4DBD, PIP, ZFHD1 from a large number of candidates. For the second idea, we utilized a modified 3-tendem Cys2-His2 ZF as protein chassis. By replacing the DNA-interactional amino residues on ZF modules, we can generate RE-specific mammalian synthetic ZF (SynZF).
<div class="block main-text">
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<center><img width="700px" src="https://static.igem.org/mediawiki/2017/8/8e/Figure1.jpg"></center>
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<div class="block main-text main-text">
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  <h class="bold-text"></br></br>Limited treatment cannot suit all cases</h>
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   <p>Carcinogenesis is a gradual progress driven by the accumulation of mutations. Tumor cells are highly heterogeneous in their surface tumor antigen expression<sup>(1)</sup>, thus immune resistance<sup>(2)</sup>, sensitivity to the treatment and so on. Meanwhile, efficient recognition by immunotherapy, as one of the fundamental challenges for solid tumors, is still in the way comparing with exciting results shown in treating hematological cancers<sup>(3)</sup>.Currently, most existing immunotherapies exhaust in trying multiple methods to improve recognition<sup>(4-6)</sup>, without considerating tumor heterogeneity. They focus narrowly on finding an ideal tumor antigen as the target and hope to generate a effective therapeutic response – monotonic response.We believe these conventional one-size-fits-all immunotherapies cannot adapt itself to all complex disease occasions in various types of tumors.<font color="#004a84">(Figure 1B)</font></br>
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</p>
 
</p>
</div>
 
  
  
<div class="block main-text notation ">
 
  <h class="bold-text dark-blue fold-trigger1"></br></br></br><i>Read more: Current methods to improve recognition and their imperfections</i></h>
 
  <div class="folded">
 
    <p><br/>
 
<h class="bold-text dark-blue">Current methods to improve recognition are not perfect</h>
 
</br>Emerging methods to improve recognizing precision, like dual recognition <sup>(6,7)</sup>and tunable sensitivity <sup>(5)</sup>, have been proved capableof eliminating specific tumor cells. However,these methods cannot completely solve the problem.
 
<br></p>
 
<p>
 
<h class="bold-text dark-blue">Specific tumor antigens for dual recognition is hard to find</h>
 
</br>The first step for immunotherapy is to select a highly specific tumor antigen as the target. However, qualified candidates for tumor antigens are rare in most cases. Taking HCC (hepatocellular carcinoma) as an example, although HCC-associated antigens, like EpCAM<sup>(8)</sup>, NY-ESO-1<sup>(9)</sup>, and GPC3<sup>(10)</sup>, are potential targets of cellular immunotherapies for advanced HCC. However, only GPC3, is wildly accepted as the tumor antigen of HCC owing to its high specificity.<sup>(6,11,12)</sup>. Only one tumor antigen for HCC prevents the use of dual recognition.
 
</br>
 
</p>
 
<p>
 
<h class="bold-text dark-blue">Tunable sensitivity requires optimized scFv– it is very get</h>
 
</br>The affinity of single-chain variable fragment (scFv) is essentialfor recognition. Even though recently highthroughput methods have been developed to screen forscFvs with different affinity to the same antigen<sup>(13)</sup>, specialized knowledge and high expense render it impossible to perform inall laboratories. Only one or two laboratories around the world have the capability to develop scFv with tunable sensitivity.
 
</p>
 
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<div class="block main-text">
 
  <h class="highlight-title dark-blue" id='remedy'></br></br></br></br>One important theory of traditional Chinese medicine:</br>suit the remedy to the case</h>
 
 
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   <h class="highlight-title dark-blue" id="Antigen"></br></br>The advantages of SynTF-SynPro</h><h2> </h2>
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1. It is a unified design for applying both natural DBDs and artificial SynZFs as DBDs on SynTFs.
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  <p>Tumor in different states need different treatments. To develop rational combined therapy, the key question is how to accurately manifest tumors’ condition. Fortunately, with improved understanding of oncogenesis and emerging therapies, clinical trials of rational combined therapy have become possible<sup>(14,15)</sup>. Through investigation, we found that antigen density heterogeneity, tumor antigen level and expression pattern are associated with disease progression<sup>(16)</sup>.Thus, Antigen density heterogeneity could be used to develop rational combined immunotherapy.</br></br>
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  <h class="bold-text">Here, we report the “SwordS”, SynNotch-Stripe system, which can spontaneously generate non-monotonic responses by targeting different surface tumor antigen density of tumor cells at different states.<font color="#004a84">(Figure 2)</font></br>
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        <img width="420px" src="https://static.igem.org/mediawiki/2017/b/b0/Figure2.jpg">
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<div class="block main-text main-text">
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   <h class="highlight-title dark-blue" id='SharpBlades'></br></br></br>SwordS enables antigen density dependent </br>tri-response for therapeutic applications</br></h>
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  <h class="bold-text"></br>SwordS consists of two main modules, SynNotch and Stripe, and one supportive module, SynTF-SynPro<font color="#004a84">(Figure 3)</font>. </br></br>
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</h>
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  <div>
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  <center><img width="700" src="https://static.igem.org/mediawiki/2017/5/59/Figure3.jpg"></center>
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<div class="block main-text main-text">
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  <h class="highlight-title dark-blue"></br></br></br>Module 1: SynNotch</br></h>
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  <h class="bold-text"></br>SynNotch,an engineered transmembrane receptor, bridges intra and extracellularinformation.</h>
+
  <p>Synthetic Notch (SynNotch)<sup>(17)</sup>consists of three parts, the synthetic extracellular recognition domain (SynECD, e.g.scFv), the core transmembrane domain of wild Notch receptor<sup>(18)</sup>, and the synthetic intracellular transcriptional domain (SynICD, e.g.SynTF). When the SynECD binds to its targeting surface antigen, induced cleavages take place on the core transmembrane domain of SynNotch, releasing the SynICD. The SynICDwould be transported into nucleus and activate the transcription of its corresponding promoter <font color="#004a84">(Figure 4)</font>. </br>
+
 
</p>
 
</p>
  <h class="bold-text"></br>SynNotch is an ideal platform for customized antigen sensing behavior. </h>
 
 
<p>
 
<p>
SynNotch provides us an exciting platform for sensing and treating tumor because its SynECD and SynICD are both customizable. SynECDcan be designed based on current available scFvs for different tumors such as α-GPC3 for HCC<sup>(11, 19)</sup>,α-Her2 for glioma<sup>(4)</sup>,α-CD19for acute lymphoid leukemia<sup>(20)</sup>, etc.SynICD will trigger customized output after SynECD recognition.
+
2. It is a tunable design as you can adjust the silencing or activating fold by different repeats of REs.
 +
</p>
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<p>
 +
3. It is a universal design because ZF is a highly modular motif. You can design more than 4<sup>9</sup> specific SynZF–RE pairs theoretically.  
 
</p>
 
</p>
  <div>
 
  <center><img width="700" src="https://static.igem.org/mediawiki/2017/d/d1/Figure4.jpg"></center>
 
  </div>
 
</div>
 
  
 
 
<div class="block main-text main-text">
 
  <h class="highlight-title dark-blue">Module 1: Module 2: Stripe</br></h>
 
  <h class="bold-text"></br>Stripe consists of 3 interactional circuits. </h>
 
  <p>SynPro S, an activating-form promoter triggered by the existence of initial signal (S), is the start point of the whole module. Meanwhile, activation strength of Promoter S (Pro S) is positively correlated with the concentration of S.SynTF X1/2, SynTF Y, are two orthogonal silencing-form synthetic transcription factor (SynTF) and their corresponding silencing-form synthetic promoter (SynPro) are SynPro X and SynPro Y. (SynTF X1 and SynTF X2 are the same transcription factor on two different open reading frams.)Importantly, the inhibition threshold of SynTF X must be much higher than SynTF Y. A, B, C are three response factors<font color="#004a84">(Figure 5A)</font></p>
 
<p>When S’s concentration is none or low. Expression level of circuit ①is low. Concentration of SynTFX1 and Y are not sufficient to inhibit SynPro X or SynPro Y. In this condition, the expression level of Circuit ②is normal.Thus,SynTF X2, the product of circuit ②, is in high concentration to sufficiently inhibit SynPro X and inhibit the expression of circuit ③ <font color="#004a84">(Figure 5B)</font>. Only A (in green) is produced.
 
</p>
 
<div>
 
  <center><img width="700" src="https://static.igem.org/mediawiki/2017/d/d6/Figure5.jpg"></center>
 
  </div>
 
<p>When S’s concentration is mediam. Expression level of ① circuit is mediam. Produced SynTF X1 is still not sufficient to inhibit high-threshold SynProX. However, SynTF Y produced by circuit ① can significantly inhibit low-threshold SynPro Y to express circuit ②. SynPro X cannot be inhibited by either SynTF X1 (not sufficient) or SynTF X2 (inhibited)<font color="#004a84">(Figure 5C)</font>. Only B (in red) is produced.
 
</p>
 
<p>When S’s concentration is high. Expression level of ① circuit is high. Both SynTF X1 and Y are in high concentration. Expression of circuit ② and ③ are inhibited<font color="#004a84">(Figure 5D)</font>. C (in blue) is massively produced. C can have a slight couple-expression with X1/Y, when S’s concentration is low or mediam. However, these expressions can be neglected comparing to the dominantly expressed A (in low concentration of S) or B (in mediam concentration of S).
 
</p>
 
 
</div>
 
</div>
  
 
<div class="block main-text">
 
  <h class="bold-text"></br>Stripe achieves combined immunotherapy through an adjustable signal sorting module. </h>
 
</div>
 
  
 
<div class="block main-text main-text">
 
<div class="block main-text main-text">
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   <h class="highlight-title dark-blue" id="Antigen"></br></br>Attention</h><h2> </h2>
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<p>
 
<p>
Stripe can spontaneously generate tri-response depending on the intensity of its input: a low intensity plateau, a hump-like signal peak for medium intensity, and a high intensity plateau <font color="#004a84">(Figure 6)</font>.In a tumor therapy oriented project, we can separately designate the three outputs as no therapeutic factor expression, therapeutic factor I expression, and therapeutic factor II expression. That’s to say, if the input intensity is medium, the output tends to be therapeutic factor I. If the input shifts towards high intensity, the output shifts to therapeutic factor II, and if the input shifts towards low intensity, output nothing. Thus, normal cells with low surface antigen signal could be ignored, reducing the off-target effect. Meanwhile, the expression of therapeutic factor I or II can be adjusted via the signal sorting module to suit different tumor conditions.
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Cause the following reasons, actually functional SynZFs are much less than 4<sup>9</sup>: </p><p>
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1. one unit SynZF motif cannot recognize all the permutation of 3 consecutive bases. </p><p>
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2. SynTF are probably not all complete orthogonal to each other. </p><p>
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3. RE repeats on SynPro can influence the function of chassis promoters. </p><p>
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Thus, before you applying our idea into your project. A pilot test is strongly needed.
 
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<td>
 
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        <img width="420px" src="https://static.igem.org/mediawiki/2017/0/05/Figure6.jpg">
 
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  </table>
 
 
</div>
 
</div>
  
 
<div class="block main-text main-text">
 
<div class="block main-text main-text">
   <h class="bold-text"></br>Develop Stripe with dynamic modelling </h>
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   <h class="highlight-title dark-blue" id="Antigen"></br></br>See More</h><h2> </h2>
  <p>To generate an antigen density-dependent tri-response pattern for SwordS, designing the gene transcription network in Stripe plays a central role. Traditional method to analyze a gene transcription network uses Hill Equation to describe the relation between each pair of transcription factor and its recognition site. However, since its parameters are substantially statistical, Hill Equation cannot provide enough accuracy and flexibility. We build up a Probabilistic Model and apply it to gene transcription network. Our model reveals the relationship between the inherent randomness and phenotypical properties of biochemical reactions in cell nucleus. We achieve high accuracy and flexibility when modelling a gene transcription network for Stripe development. To provide further insights, we have created an online software to enable you to design and analyse your own gene transcription network dynamically.
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<p>
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Integrated information about Part Collection posted on <a href="https://2017.igem.org/Team:Fudan/Demonstrate">Demonstrate</a>: Wiring orthogonal and tunable SynTF-SynPro repertoire. You cannot miss it.
 
</p>
 
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<p>
  
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We listed Biobricks belong to Part Collection below.
  
<div class="block main-text main-text">
 
  <h class="highlight-title dark-blue"></br></br></br>Module S: SynTF&SynPro</h>
 
  <p></br>In silico modeling indicates that the key criterion for functional Stripe construction was the matching of orthogonal SynTF X and SynTF Y that enabled sufficient separation of the low and high thresholds. Although previous published workshas reported a synthetic Stripe-like circuit in bacterial<sup>(21)</sup> or in mammalian<sup>(22)</sup> cells,a tunable system has not yet been created. Their output responses to signal intensity are relative fixed, which means they response to high, moderate, and low levels of input with constant intervals. However, tunable intervals should be built so that the system can be tuned to against tumor antigen with heterogeneity.We created and characterized SynTF-SynProto response to desired intervals. This set is a powerful toolbox to construct customized signaling sorting characteristics.
 
</p>
 
</div>
 
  
<div class="block main-text main-text">
 
  <h class="sup-title dark-blue" style="text-align:center;" ></br></br></br></br></br>SynNotch + Stripe </h>
 
  <h class="sub-title dark-blue" style="text-align:center;"></br>combining these two sharp blades, with the support of SynTF-SynPro, SwordS is a promising platform for the next generation cellular immunotherapy.</h>
 
</div>
 
 
<div class="block main-text main-text">
 
  <h class="highlight-title dark-blue" id='HCC'></br></br></br>The opportunity of applying SwordS to treat HCC</h>
 
  <p></br>Liver cancer, including HCC (hepatocellular carcinoma), is an extraordinarily heterogeneous disease because of its diversity. As a result, individualized therapy isgreatly needed<sup>(23)</sup>. Antigen expression pattern is related to HCC progression and prognosis. High expression of HCC-associated tumor antigen was associated with better prognosis(16):EpCAMwhose positive or negative expression can be an indicator to distinguish HCC subtype<sup>(24)</sup>and the expression of GPC3 is more frequently observed in moderately or poorly states HCC than in well state one<sup>(25)</sup>.Executing combinationalimmunotherapy is believed to be a dramatic improvement of treatment to HCC<sup>(26, 27)</sup>. With SwordS and the known tumor antigen GPC3, we propose to release therapeutic factor I when GPC3 is mediam and release therapeutic factor II when GPC3 is high. For example, when the expression of tumor antigen is high, the acquired immune system is easier to identify tumor, a therapeutic factor which can enhance acquired immune system might generate a better therapeutic effect; a therapeutic factor which can enhance inherent immune system might have a better effect when the tumor antigen expression is low. Thus, weassumethat designating therapeutic factor I as IL-12 (which can drive potent innate immune responses to cancer) and designating therapeutic factor II as IL-18 (which can promote CD8<sup>+</sup> T cells is a rational combination for SwordS.
 
</p>
 
  <p>When the expression of the tumor antigen is high, acquired immune system is relatively easy to identify tumor cells, a therapeutic factor which can enhance acquired immune system might be beneficial for the treatment. Thus, we propose IL-18 as the designating therapeutic factor II, which is secreted protein and promotes the proliferationof CD8<sup>+</sup> T cells<sup>(28)</sup>. When the tumor antigen expression is mediam, expressing a therapeutic factor that can enhance innate immune system and facilitate the recognition by acquired immune system might be better. Thus, we propose IL-12 as the designating therapeutic factor I, which could drive potent innate immune responses to cancer<sup>(29)</sup>. In summary, with SwordS, we are able to differential express either IL-12 or IL-18 depending the surface antigen destiny, to strategically kill tumor cells
 
 
</p>
 
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<div class="block main-text main-text">
 
  <h class="highlight-title dark-blue"></br></br></br></br>Demonstration</h>
 
  <p></br>We did a lot of workto demonstrate the feasibility of our project and preliminarily characterized SynTF-SynPro set.
 
</p>
 
  <h class="notation dark-blue"><a href="https://2017.igem.org/Team:Fudan/Demonstrate">◆Click here to see experimental data and prediction from dynamic modelling.</a></h>
 
</div>
 
  
<div class="block main-text main-text">
 
  <h class="highlight-title dark-blue" id='Postscript'></br></br></br></br></br>Postscript Note</h>
 
  <p></br>We believe SwordS is a universal solution for various cancers. When we need to demonstrate our idea in one specific cancer, we picked the one with highest risk for Chinese popultion, HCC.
 
</p>
 
  <h class="notation dark-blue"><a href="https://2017.igem.org/Team:Fudan/HCC">◆Clic here to see more information about HCC.</br></a></h>
 
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<table class="tg" width="60%" style="border-collapse:separate; border-spacing:2px 10px;">
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    <th colspan="2"><b>SynTFs</b></th>
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    <th colspan="2"><b>SynPros</b></th>
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  </tr>
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  <tr>
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    <td>Gal4-KRAB(TF-KRAB-1)</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446037”>(BBa_K2446037)</a></td>
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    <td>Sv40-UAS(Sv40-UAS)</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446036”>(BBa_K2446036)</a></td>
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  </tr>
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  <tr>
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    <td rowspan="3">ZF_PIP_KRAB(TF-KRAB-2)</td>
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    <td rowspan="3"><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446045”>(BBa_K2446045)</a></td>
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    <td>SV40_2_PIP</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446033”>(BBa_K2446033)</a></td>
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  </tr>
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  <tr>
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    <td>SV40_4_PIP</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446034”>(BBa_K2446034)</a></td>
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  </tr>
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  <tr>
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    <td>SV40_8_PIP</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446035”>(BBa_K2446035)</a></td>
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  </tr>
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  <tr>
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    <td>ZF_21-16KRAB(TF-KRAB-3)</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446039”>(BBa_K2446039)</a></td>
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    <td>SV40_8_ZF_21-16</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446030”>(BBa_K2446030)</a></td>
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  </tr>
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  <tr>
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    <td>ZF_42-10_KRAB(TF-KRAB-4)</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446040”>(BBa_K2446040)</a></td>
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    <td>SV40_8_ZF_42-10</td>
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    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446025”>(BBa_K2446025)</a></td>
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  </tr>
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  <tr>
 +
    <td rowspan="3">ZF_43-8_KRAB(TF-KRAB-5)</td>
 +
    <td rowspan="3"><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446041”>(BBa_K2446041)</a></td>
 +
    <td>SV40_2_ZF_43-8</td>
 +
    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446026”>(BBa_K2446026)</a></td>
 +
  </tr>
 +
  <tr>
 +
    <td>SV40_4_ZF_43-8</td>
 +
    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446027”>(BBa_K2446027)</a></td>
 +
  </tr>
 +
  <tr>
 +
    <td>SV40_8_ZF_43-8</td>
 +
    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446028”>(BBa_K2446028)</a></td>
 +
  </tr>
 +
  <tr>
 +
    <td>ZF_54-8_KRAB(TF-KRAB-6)</td>
 +
    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446042”>(BBa_K2446042)</a></td>
 +
    <td>SV40_8_ZF_54-8</td>
 +
    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446029”>(BBa_K2446029)</a></td>
 +
  </tr>
 +
  <tr>
 +
    <td>ZFHD1_KRAB(TF-KRAB-7)</td>
 +
    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446043”>(BBa_K2446043)</a></td>
 +
    <td>SV40_4_ZFHD1</td>
 +
    <td><a href=http://parts.igem.org/wiki/index.php?title=Part:BBa_K2446032”>(BBa_K2446032)</a></td>
 +
  </tr>
 +
</table>
  
 
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Latest revision as of 23:47, 1 November 2017

Part Collection

As a team focusing on real-world problem, we found it is hard to obtain sufficient mammalian Biobricks on the Registry of Standard Biological Parts comparing to the convenience for project in bacteria. In synthetic biology, one central route is to construct a controllable biological network, and electing suitable transcription factor and corresponding promoter is vital.

The best way to predict the future is to invent it. As we couldn’t find Biobricks that were completely satisfying to us, we just invent it.

For this year’s iGEM competition, we present an approach to design customized mammalian synthetic transcription factor (SynTF) - synthetic promoter (SynPro) pairs. This set is a powerful toolbox to construct customized and orthogonal transcriptional network.



How to design SynTF-SynPro

SynTFs enable binding to user-specified DNA sequences, response element (REs), on SynPros then silencing or activating their transcription. The SynTFs we designed were in an unified style containing three core domains from N-terminal to C-terminal: DNA binding domain (DBD), nuclear location sequence (NLS), transcription regulating domain. We chose (G4S) as linker to be added between DBD and SV40 NLS for region flexibility. We could choose KRAB or VP64 as transcription regulating domain to construct silencing- or activating-form SynTFs (SynTF(S)s and SynTF(A)s). The structures of their corresponding silencing- or activating-form SynPros (SynPro(S)s and SynPro(A)s) were pSV40-N*RE or N*RE-minCMV.

The critical step to find optional SynTF group is to find enough differently specific and orthogonal DBDs. We applied two approaches to achieve this. Firstly, we widely investigated those commonly used DBD originating from different species. Secondly, we devised a platform based on artificial zinc-finger (ZF). For the first idea, we chose Gal4DBD, PIP, ZFHD1 from a large number of candidates. For the second idea, we utilized a modified 3-tendem Cys2-His2 ZF as protein chassis. By replacing the DNA-interactional amino residues on ZF modules, we can generate RE-specific mammalian synthetic ZF (SynZF).



The advantages of SynTF-SynPro

1. It is a unified design for applying both natural DBDs and artificial SynZFs as DBDs on SynTFs.

2. It is a tunable design as you can adjust the silencing or activating fold by different repeats of REs.

3. It is a universal design because ZF is a highly modular motif. You can design more than 49 specific SynZF–RE pairs theoretically.



Attention

Cause the following reasons, actually functional SynZFs are much less than 49:

1. one unit SynZF motif cannot recognize all the permutation of 3 consecutive bases.

2. SynTF are probably not all complete orthogonal to each other.

3. RE repeats on SynPro can influence the function of chassis promoters.

Thus, before you applying our idea into your project. A pilot test is strongly needed.



See More

Integrated information about Part Collection posted on Demonstrate: Wiring orthogonal and tunable SynTF-SynPro repertoire. You cannot miss it.

We listed Biobricks belong to Part Collection below.

SynTFs SynPros
Gal4-KRAB(TF-KRAB-1) (BBa_K2446037) Sv40-UAS(Sv40-UAS) (BBa_K2446036)
ZF_PIP_KRAB(TF-KRAB-2) (BBa_K2446045) SV40_2_PIP (BBa_K2446033)
SV40_4_PIP (BBa_K2446034)
SV40_8_PIP (BBa_K2446035)
ZF_21-16KRAB(TF-KRAB-3) (BBa_K2446039) SV40_8_ZF_21-16 (BBa_K2446030)
ZF_42-10_KRAB(TF-KRAB-4) (BBa_K2446040) SV40_8_ZF_42-10 (BBa_K2446025)
ZF_43-8_KRAB(TF-KRAB-5) (BBa_K2446041) SV40_2_ZF_43-8 (BBa_K2446026)
SV40_4_ZF_43-8 (BBa_K2446027)
SV40_8_ZF_43-8 (BBa_K2446028)
ZF_54-8_KRAB(TF-KRAB-6) (BBa_K2446042) SV40_8_ZF_54-8 (BBa_K2446029)
ZFHD1_KRAB(TF-KRAB-7) (BBa_K2446043) SV40_4_ZFHD1 (BBa_K2446032)