UPDATE 09/18/2013

why liver?

Liver cancer is the fifth deadly cancer in the world and the situation is more serious in China as 55% of the patients are from China. Every year, thousands of patients wait for liver transplant to save their lives. Recent advances in iPS-derived hepatocytes provides an easier and more convenient way to solve the problem of donor shortage and reduce immune reaction. iPS-derived hepatocytes are also required for scanning for hepatic toxicity with the advantages of batch to batch stability and more resources. What's more, patients with inherent metabolic diseases can benefit from iPS-derived hepatocytes with genetic information modified. Here, we choose the iPS-derived hepatocytes as a model to test our idea. We have selected the liver-specific miR-122 as a marker to distinguish normal, differentiated liver cells from undifferentiated or cancerous cells. Our device provides a solution to increase the efficiency of directional differentiation and prevent possible carcinogenesis.

For more information, please go to the background page.

why miR-122?

MicroRNAs can regulate gene expression and control many important process including development, differentiation, apoptosis and proliferation. They regulate gene expression by binding to a short 6 nt region within the 3’UTR of their target mRNAs.

MicroRNA-122(miR-122) is a liver-specific microRNA that is most abundantly expressed in the liver as it accounts for approximately 70% of all hepatic icroRNAs. Interestingly, it is specifically highly expressed in normal hepatocytes instead of undifferentiated or cancerous cells. According to this, we have designed a complementary miR-122 target as a sensor to select the healthy hepatocytes we want when high level of endogenous miR-122 bind to our target in 3'UTR and then degrade the mRNA of suicide gene. That is to say, during direction differentiation, undifferentiated or wrong kinds of cells will express the suicide gene because they have low level of miR-122. iPS-derived hepatocytes do not express deadly level of suicide gene unless it becomes cancer cells soontaneously.

For more information please go to the background page.

Which suicide gene?

Why suicide gene?

In our project, we try to build a circuit that can prevent the iPSC-differentiated tissues from tumor formation. Instead of using some medicines to kill them, like the traditional gene therapies did, what we want to achieve here is to make the tumor cells kill themselves, in other word, automatically commit suicide. So we decided to use an exogenous suicide gene.

The ideal suicide genes that fit our design here will be genes that can successfully induce apoptosis in cells and do not introduce any harmful effect to normal tissues. However, many apoptosis pathways are reported to be blocked in tumor cells. From recent reports and papers, we found out that there have been many genes reported to have important roles in mammalian cell apoptosis. After a long time comparison and consideration, our final candidates of suicide gene are listed below:

- hBax & hBax mutant

- delta TK

- caspase3

- rip1

- rip3

- apoptin

The introduction of each genes about its suicide mechanisms and the reasons why we choose them are as follows:

Which suicide gene?

hBax & hBax mutant

hBax is a member of the Bcl-2 related protein family from human. This Family contains pro-apoptotic and anti-apoptotic proteins, and the balance among them determines the cell survival. hBax is the pro-apoptotic protein. During apoptosis, hBax will be inserted into the mitochondrial outer membrane and form permeable channels, release pro-apoptotic signals, finally lead to apoptosis[1]. The pathway of apoptosis is showed in Figure 1.

Figure1. apoptosis pathway induced by hBax

hBax S184a[3] is a mutant of hBax that can constantly insert into mitochondrial outer membrane, thus we guess that it may have a stronger apoptosis-induced effect than normal hBax.

It have been reported that over expression of this gene can successfully induce apoptosis in both Hela cell line and HEK-293 cell line[2]. Due to its generality, we finally determined to use it as one of our suicide genes candidates.

However, our experiments results finally showed to us that, when expressed in Hep G2 cell line, which is a typical hepatoma cell line, they can not induce observable apoptosis. However, although it can not successfully kill Hep G2 cell line, we figured out that the pathway is conserved in yeast[4] ,so we also tried to transfect the gene and its mutant in yeast and finally proved that the killing effect is observable and even dose-dependent (BBa_K1061006). So this extra result may be useful for other team in the future who want to apply safety device in yeast. We finally submitted the hBax as a biobrick and its mutant form as an improvement of the pre-existing part of part registry.

(show results)

Caspase 3

Caspase 3 is the last downstream executer of apoptosis in most mammalian cells. Almost every apoptosis process needs the execution of caspase 3. As a cysteine protease, it can directly cleavage proteins inside cells and take part in DNA fragmentation[4]. Caspase 3 contains two subunits, p17 and p12, which are translated in the same ORF. When cleavaged by caspase 9, another kind of protease involving in apoptosis, they will form a dimer that will act as an active form[5].

Actually we split its gene into two parts, p17 and p12, and we used leuzine zipper to direct the dimerization of the two subunits[5].

However, in our project we finally decided to drop trying this gene, mainly for 3 reasons:

1. The apoptotic effect needs two subunit to be expressed simultaneously, which would increase the complication of our circuit.
2. To overcome the anti-apoptotic protein XIAP[6], which is high-expressed in Hep G2 cell line[7], we may need an extremely high expression of caspase 3, which would also be a problem for our experiment.
3. We have mistakenly clone the wrong ORF of two subunits from the plasmid, so it leave us no time to do the experiment of caspase 3 before regional jamboree=.=.

Besides, we may try to test another version of active caspase 3---the reconstitute caspase 3 [8]in following days.

RIP 1

RIP1 is the abbreviation of Receptor Interacting Protein kinase 1 in mammalian cells. It is an important regulator of cell survival and death, taking part in several program cell death pathways[9]. It has been reported that over expression of RIP 1 can induce both apoptosis and necrosis[10] in certain cell lines. So it is a potential suitable suicide gene that we can use in our device.

We tested rip1 in several cell lines, including HTC-75, Bosc, and Hep G2 cell lines. What we have observed is a mix of both apoptosis and necrosis( result ). Although it can induce necrosis in cancer cell lines, which may potentially cause inflammation in tissues, we still consider it as our choice of suicide gene. The reasons are as follows:

1. We know that in iPSC differentiation period, only a small fraction of cells will become cancerous at a certain time, so the necrosis of these cells would not likely to lead to severe inflammation.
2. Many apoptosis pathways have been reported to be blocked in tumor cells, but there is some evidence revealing that when the apoptosis pathways are blocked the necrosis pathway will be activated[11]. Besides, some recent papers showed that RIP1 can trigger cell necrosis only with extra exogenous medicine. In other circumstances RIP1 could lead to apoptosis.
3. We have cloned another receptor interacting protein kinase, RIP 3, which has been proved to interact with RIP 1 and lead to necrosis[12], so we think that even the over expression of RIP 1 can not successfully kill the cells, it may also co-express with RIP 3.

Surely, we will keep trying to find genes that only lead to apoptosis but not necrosis in the future, the better solution, in our mind, may be a combination of multiple apoptotic genes.

RIP 3

　　 RIP3, like RIP 1, is also a member of Receptor Interacting Protein family. It works via the interaction with RIP 1, and thus induces the necrosis pathway which RIP 1 mediated.[1]

However, it have also been reported that over expression of RIP 3 in certain cell lines can induce apoptosis[15].In our experiment, we found out that RIP 3 can lead to cell death in several cell lines, including HTC-75 cell lines and HEK-293 cell lines.

Because RIP 3 mainly induces necrosis, we select it as our candidate of suicide genes for the same reasons as we select RIP 1. And we also suggest that when using RIP 3 to cure cancer, tight control expression system may be necessary.

Apoptin

Apoptin, a protein first isolated from Chicken anemia virus, has been regarded as a potential drug for cancer treatment[16]. It has been reported in over 70 cell lines that apoptin can selectively kill cancer cells but not normal cells[17]. The result of in vivo test in mice is very exciting: the intraperitoneal injection of vector carrying the apoptin seems not confer any observable side effect on mice[18].

The mechanism of how apoptin works is not fully understood. It probably works via the non-p53 apoptosis pathway[17],hence is not easy to be blocked. The localization of apoptin in cancer cells is in nuclear, while in normal cells it locates in cytoplasm[17] . This was proved by our experiment results.

A special character of apoptin is that it works like a sensor, probably by recognizing certain early signals of cancer formation[17]. These signals may be general, which explained the reason why the apoptin can kill such a broad spectrum of cancer cells. So the construct of EF-1alpha-apoptin may provide a general circuit for safety issues of gene therapy and renew the concept of sensor. Making use of the by-stander effect, TAT-apoptin[20] or SP-TAT-apoptin[21] may be powerful and provide a "safe environment" for the cells under genetic manipulation.

However, we still have to say that although Apoptin has been proved to be safe for many normal cell types, it has not been proved in all normal cell types. So we should consider and test thoroughly about the immune reaction effect, making sure that it does not happen or can be controlled.

Delta TK:

TK is the abbreviation of thymidine kinase from HSV(Herpes simplex virus). It can convert the non-toxic prodrug ganciclovior into toxic product that can incorporate into replicating DNA strand and finally lead to apoptosis in cancer cells[22].

Due to its bystander effect, TK expression in cancer cells under the ganciclovior treatment may also hurt the normal cells in neighborhood[23]. So we use a truncated version that won't lead to apoptosis[24].

However, due to several reasons including its drug inducible property and the time limit, we haven't try this gene yet. We may do it in the following days, and its drug inducible property may bring some advantages in some circuit design.

Future work: Combination of suicide genes? Or using the scalable miRNA circuit?

With our project proceeded, we found out that apoptosis pathways are generally blocked in cancer cell lines (maybe this's one of the reasons why cancers are so hard to deal with). However, Synthetic biology has a great advantage in designing complicated circuits, and hence, it will be possible to combine several suitable suicide gene together and construct a circuit that can overcome the blocking problem of apoptosis pathway in cancer cells. And by screening the publication work we also found out that the shRNA and miRNA expression technique, which is controllable[1][2], can successfully knock-down gene expression.

The circuit design based on shRNA and miRNA should be scalable, because the sequence of them are short enough so that the whole circuit can be much more complicated than the design base on suicide proteins. The broader target of miRNA and shRNA is, the harder to be blocked. For this reason, the short RNA -based circuit, including CRISPRi[27], may be a promising way for cancer treatment and gene therapy design.

Which Tet system?

Why Tet system?

The aim of our project is to ensure the safety of iPS-derived cells for tissue transplant. According to our design, cells other than normal, differentiated hepatocytes are condemned to death. There are two candidate time periods for device integration: before iPSCs induction and after the generation of iPSCs. Anyway, the safeguard device is likely to be intergrate before the final phase of differentiation because hepatocytes are resistant to transfect. But our device might also kill these cells. how to keep primitive cells with low level of miR-122 alive until differentiation is finished? With a Tet system, we can turn off the device and let cells go through a normal process of amplification and diffentiation before final selection.

What is Tet control system?[1][28]

Tet control system is a beautiful combination of prokaryotic and eukaryotic gene-expression regulatory system. It consists of two parts: the regulatory protein tTA or rtTA and a downstream response element. TetR is a repressor from E. coli, which can block the downstream expression when it binds to a TetO operon. When tetracycline(Tc) or doxycycline(Dox) is absent, gene expression is repressed and when Tc or Dox is introduced to the medium, it leaves the TetO site and let the gene of interest express. The whole tTA regulatory protein is fused by TetR and an activation domain VP16, which will still bind to TetO when dox is absence. However, by alternating four amino acids of tTA, which called rtTA, it binds to tetO operon when Dox is present. When the 7 consecutive tetO sequences are fused with a minimal CMV promoter, we will get a regulatory promote, TRE, that is activated when tTA or rtTA binds to it.

Which kinds of Tet-control system?

1.On or off, this is a question.

Basically, there are two kinds of tet control system. The first one, tet-off, is based on tTA, which will activate downstream expression when Tc or Dox is absence. The second one,tet-on, is based on rtTA, which will activate downstream expression when Dox is added.

So, which one should we use?

Our construction need to express the suicide gene when detecting the cells are cancerous. So the tet part should be activated in vivo, only suppressed by the miRNA-122. After the transplantation, it will be inconvenient to intake dox constantly, because dox is somehow, a kind of antibiotics. Also, To intake dox after transplantation will need higher dose of dox to achieve the same level of expression, comparing to add dox into culture medium. So, the better choice will be using tet-off system, which can achieve constantly expression without adding dox. For preventing the expression of suicide gene in iPS cells, we only need to add dox during the in-vitro differentiation.

However, combining a special suicide gene apoptin, which will not kill normal cells when constantly expressing, with another suicide gene, it is possible to use tet-on system without constantly intake the dox in vivo. And the time of adding dox will be shorter.

For this consideration, we also test the tet-on expression system in our experiment. Unforturnately, the latest result that we got shows that apoptin maybe harmful to iPS cells. But, this kind of construction may still be used in other kinds of stem cells, for instance, the adipose-derived stem cells.

2. One, two, three: which is the golden generation?

There are 3 generations of tet-expression systems now.

We expect that our suicide gene has low level of leakage expression and a high fold increasement. First, we want to find out the one with lowest leakage expression. It turns out to be tTA+p_tight. However, a low leakage expression is usually in accompany with low maximal expression. Hence, transient transfection sadly prove that the suicide gene is not strong enough to kill all cells. But cells escaped from surveillance might go through rapid genetic rearrangement to acquire invasiveness. Actually we have another type of Tet-off system fused with KRAB transcription factor. It has a higher leakage expression but the fold increasement is the best. Actually, this problem can be circumvent in the process of generating stable cell lines because leakage expression differs from clone to clone and is lower than in transient transfection. However, KRAB does not function in ES cells and this Tet-off is abandoned. We are also interesting in alternative Tet system like those controlling the expression of RNA and the else.

Another tet- systems that we notice are the systems that induce the expression of miRNA[33] or shRNA[34]. We have discuss the possible use of miRNA and shRNA in constructing gene therapy and safeguarding circuit, so we will pay attention to these systems in the future. (Show figures)

Why EF-1α promoter？

To consistently express the protein tTA of our circuit in a high level, we finally select a human elongation factor 1 alpha ( PEF1α ) to replace the original promoter pCMV to be our promoter in tet-off system.

Generous & strong

Since Elongation Factor 1α takes part in translation[1]，almost every types of mammalian cells need to express this factor. Hence its promoter, EF-1alpha, is constantly activated no matter what kind of state the cell is undergoing. In our design, the expression of our device is supposed to be stable and persistent during the whole differentiating process, so we choose EF-1alpha promoter to drive tTA transcription. Besides, EF-1alpha promoter is one of the strongest promoters that has been used in constructing mammalian circuit[2].

Without being silenced in PSCs

EF-1alpha promoter has been proved to be particularly useful in constructing stable cell lines[2]. Compared to another strong promoter, CMV promoter, which has also been widely used in constructing mammalian circuit, EF-1alpha promoter won't undergo transgenic silence in certain cell types, including the iPS cells in our project and hematopoietic stem cells et al[3].

Previous work[4] has showed that the expression level of gene driven by EF-1alpha promoter is more robust in several cell lines, which will provide convenience to construct general circuit used in different cell lines. The data that characterize in one type of cell lines will be reliable in other types.

(Figure from reference [4])

Why lentivral vector?

This year, we decided to use lentivirus vector to carry our circuits, deliver and long-term maintain of our circuit in our chassis genome. We will introduce the mechanism of lentiviral transfection system and the reasons why we choose it.

What is lentiviral vector?

Lentiviral vectors (LV) are viral-based gene delivery systems that can stably deliver genes or RNAi into primary cells or cell lines with up to 100% efficiency. LVs bind to target cells using an envelope protein which allows for release of the LV RNA containing the gene or gene silencing sequence into the cell. The LVs RNA is then converted into DNA using an enzyme called reverse transcriptase by a process called reverse transcription. The DNA pre-integration complex then enters the nucleus and integrates into the target cell's chromosomal DNA. Gene delivery is stable because the target gene or gene silencing sequence is integrated in the chromosome and is copied along with the DNA of the cell every time the cell divides. One of the discriminating features of LVs is their ability to integrate into non-dividing cells, in contrast to other vectors that either don't integrate efficiently into chromosomal DNA (e.g. non-viral, Adenoviral and Adenoviral-Associated vectors) or can only integrate upon cell division (e.g. conventional Retroviral vectors).

Why we choose it?

Because our device is supposed to be expressed stably in a long term and therefore persistently safeguard the cells under any condition, we finally choose lentivirus to be our delivery system into iPSCs, for its high transfection efficiency and the ability to integration into host genome. Though we can never escape the fact that the use of lentivirus could increase the oncogenic risks in cells at the same time, however, considering another fact that almost every inducing/reprogramming factors in iPSCs are oncogenes, maybe the better thing we could do here is to deliver a monitor device which would persistently safeguard the cells in a long term.

To sum up, we choose lentivirus as our delivery system mainly for the following reasons:

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• Lentivector can integrate into human genome in a multi-copy way.
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• Lentivector can stably expressed in wide types of cell lines, without being silenced or irreversible transgenic suppression in ESCs and iPSCs.
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• Lentivector has a relatively higher efficiency compared with other integrating virus.
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• Lentivector is relatively safer in all integrating virus.

The lentivector we used in our project is the 3rd generation inducible lentivirus pPRIME[1], whose packaging plasmids are psPAX2 and pMD2G. We packaged lentivirus mix in 293T cell lines.