Team:SYSU-China/Project

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<DIV class="chapter">
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<span>UPDATE <INS>09/18/2013</INS></span>
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<span>Project/Background</span>
<h1>iPSCs</h1>
<h1>iPSCs</h1>
<h2>What is iPSCs?</h2>
<h2>What is iPSCs?</h2>
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<h3>A one-way journey?</h3>
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<h3>Life there and back again</h3>
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During the first half of the 20th century, researchers always believed that the life's one-way journey also applied to cells: Once a cell has developed into a specialized cell, it would be locked into that state, and unable to return to immature, pluripotent stem cell state. Conrad Hal Waddington, a famous developmental biologist in last century, once illustrated the cellular differentiation as an epigenetic landscape in which cells are seen as marbles rolling down in valleys to reach their end-point destinations as differentiated cells. They do not normally move back towards the top of the mountain to get back to the undifferentiated state, and they are not normally crossing into other valleys to develop into unrelated cell lineages<a class="quote">[1]</a>.  
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In the past century, scientists always believed that the life's one-way journey also applied to cells: Once a cell has developed into a specialized cell, it would be locked at that situation, unable to return back to pluripotent stem cell.
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<img src="https://static.igem.org/mediawiki/2013/8/8b/Introduction_01.jpg" width="500" height="197" />
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However, this prevalent view was radically overturned in 1962, when John B. Gurdon demonstrated that the nucleus from a differentiated frog intestinal epithelial cell was capable of generating a fully functional tadpole upon transplantation to an enucleated egg<a class="quote">[2]</a>. This discovery shattered the dogma that cellular differentiation could not be a bidirectional process, but the question remained whether an intact differentiated cell could be fully reprogrammed to become pluripotent again.
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However, this prevalent view was radically overturned in 2006, when Shinya Yamanaka, a Japanese scientist who afterward shared the 2012 Nobel Prize in Physiology or Medicine with John B. Gurdon<a class="quote">[1]</a>, proved that introduction of four transcription factors into a differentiated cell was sufficient to return the cell into a pluripotent situation. In his experiment, what Yamakana did was introducing four genes encoding the transcription factors (Myc, Oct3/4, Sox2 and Klf4), which were selected to reinstate pluripotency in somatic cells to skin fibroblasts. These synthetical new stem cells were thereafter named by their Japanese father as iPSCs (induced pluripotent stem cells). A year later, using the same four transcription factors in the 2006 paper, Yamanka's group successfully produced human iPS cells.
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<img src="https://static.igem.org/mediawiki/2013/1/11/Introduction_3.png" width="500" height="198" />
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<h3>A technology with many possibilities</h3>
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<p>The groundbreaking work that Yamakana and his group did in 2006 truly opened up a completely new research field to this world. It was a paradigm-shifting fundamental breakthrough, as it firstly demonstrated that an differentiated somatic cell could be reprogrammed to be pluripotent stem cell again. iPSCs technology, a new technology with many possibilities, attracts scientists and researchers all over the world, mainly for its three unique superiorities:
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<h3>Life there and back again</h3>
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<p>
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In 2006, Shinya Yamanaka, a Japanese scientist who afterward shared the 2012 Nobel Prize in Physiology or Medicine with John B. Gurdon<a class="quote">[5]</a>, proved that introduction of a small set of transcription factors into a differentiated cell was sufficient to revert the cell into a pluripotent state. In his strikingly bold experiment, what Yamakana did was introducing 24 genes encoding the transcription factors which were considered as candidates to reinstate pluripotency in somatic cells to skin fibroblasts in one step. Surprisingly, he found out that a few of these cells actually generated colonies that showed a remarkable resemblance to ES cells. Then he reduced the number of genes capable of inducing such colonies one by one, and finally, four factors (Myc, Oct3/4, Sox2 and Klf4) were picked out, whose combination were identified to be sufficient to reprogram the skin fibroblasts to pluripotent stem cells<a class="quote">[3]</a>. These synthetical new stem cells were thereafter named by their Japanese father as iPSCs (induced pluripotent stem cells). A year later, using the same four factor combination from the 2006 paper (Myc, Oct4, Sox2 and Klf4), Yamanka's group successfully produced human iPS cells, whereas another laboratory, James Thomson's lab, achieved the same goal with a somewhat different transcription factors combination (Lin28, Nanog, Oct4 and Sox2)<a class="quote">[4]</a>.
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<img src="https://static.igem.org/mediawiki/2013/2/2a/Introduction_03.jpg" width="500" height="198" />
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<h3>A technology with many possibilities
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</h3>
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<p>The groundbreaking work that Yamakana and his group did in 2006 truly opened up a completely new research field to this world. It was a paradigm-shifting fundamental discovery, as it was the first demonstration that an intact differentiated somatic cell could be reprogrammed to become pluripotent. iPSCs technology, a new technology with many possibilities, attracts scientists and researchers all over the world, mainly for its three unique superiorities:
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<p>
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<U><EM>- No strong immunological reaction:</EM></U> Since iPS cells can be cultured from the patient's own cells, it is not quite possible to lead to immunological reaction when directionally differentiated iPSCs are transplanted after in vitro culture. While in 2011 several studies argued the weak immune reaction to transgene-free iPSCs, these arguments were subsided later by other scientists and Yamanaka himself, pointing out that "the most prominent study that reported the immunogenicity of the cells examined undifferentiated iPSCs, which will never be used in cell transplantation therapy"<a class="quote">[6]</a>. Recent work by Araki and Guha used syngeneic mouse models to demonstrate that transplanted iPSC-derived embryoid bodies, skin and bone marrow tissues engraft efficiently with almost no signs of rejection<a class="quote">[6]</a>.
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<U><EM>- No strong immunological reaction:</EM></U> Since iPS cells can be cultured from the patient's own cells, it is not quite possible to lead to immunological reaction when directionally differentiated iPSCs are transplanted after in vitro culture. While in 2011 several studies argued the weak immune reaction to transgene-free iPSCs, these arguments were subsided later by other scientists and Yamanaka himself, pointing out that "the most prominent study that reported the immunogenicity of the cells examined undifferentiated iPSCs, which will never be used in cell transplantation therapy"<a class="quote">[2]</a>.  
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<U><EM>- "Thank god we don't need embryos anymore!":</EM></U> Simultaneously, the technology of iPSC was also hailed by many commentaries as a milestone advance that solved the ethical and political problems in stem cell research field. In the past, stem cell research relied heavily of embryonic stem cells harvested from embryos. Human embryos are not easy to come by, and many people consider research involving use of human embryonic stem cells to be ethically questionable<a class="quote">[8]</a>. With no further evidence, iPSC technology not only breaks the ethical barrier of relying on using eggs or earlier embryos for deriving stem cells, but also leads to a convenient way of obtaining patient-specific stem cells.
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<U><EM>- "Thank god we don't need embryos anymore!":</EM></U> Simultaneously, the technology of iPSC was also hailed by many commentaries for it solved the ethical problems in stem cell research field. In the past, stem cell research relied heavily of embryonic stem cells harvested from embryos. Human embryos are not easy to come by, and many people consider research involving use of human embryonic stem cells to be ethically questionable. With no further evidence, iPSC technology not only “breaks the ethical barrier of relying on using eggs or earlier embryos for deriving stem cells, but also leads to a convenient way of obtaining patient-specific stem cells”<a class="quote">[3]</a>.
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<U><EM>- Wide application in different fields:</EM></U> Nowadays, scientists are making progress toward applying iPSCs in many fields. One of the applications - which has already become reality - is to use iPS cells in both analysis of disease mechanisms and investigation of potential new treatments. In the future scientists hope to be able to use iPS cells to culture cells that can be transplanted into the body and replace diseased cells. Two examples are the dopamine-producing cells in the brain that degenerate in patients with Parkinson disease, and the insulin-producing cells that die off in patients with diabetes[13]. So far, more than 100 reports published in the past three years using disease-specific iPSCs<a class="quote">[8]</a>.
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<U><EM>- Wide application in different fields:</EM></U> Nowadays, scientists are making progress in applying iPSCs in many fields. One of the applications - which has already become reality - is to use iPS cells in both analysing disease mechanisms and investigating potential new treatments. In the future scientists hope to be able to use iPS cells to culture cells that can be transplanted into the body and replace diseased cells.  
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These advances above together made the iPSC to be the "star cell" which offers immense potential as a source for regenerative therapies. However, the intrinsic qualities of self renewal and pluripotency that make these cells so therapeutically promising are also responsible for an equally fundamental tumorigenic potential, and the the intrinsic shortcomings of the current methods of inducing pluripotency even pose more uncontrollable risks on that. High rates of tumorigenicity has become a most crucial hurdle for large-scale clinical implementation of iPSC technology.
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These advances above together made the iPSC to be the "star cell" which offers immense potential as a source for regenerative therapies. However, the intrinsic qualities of self renewal and pluripotency that make these cells so promising are also causing equally fundamental tumorigenic risks, and the intrinsic shortcomings of the current methods of inducing pluripotency even pose more uncontrollable risks on that. High rates of tumorigenicity has become a most crucial hurdle for clinical implementation of iPSC technology.
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<h3>Tumorigenicity as a clinical hurdle </h3>
<h3>Tumorigenicity as a clinical hurdle </h3>
<p>
<p>
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The risks of iPSC tumorigenicity have been widely concerned over the past several years. In the study in 2009, Yamakana tested 55 mice transplanted with SNS (secondary neurospheres) from 11 TTP-iPS cell clones, 46 mice among them died or became weak within 9 weeks after transplantation because of tumors. Whereas in contrast group, the number of the tumor-showing mice transplanted with SNS derived from the ES cell clones was only 3 among 34[11]. This result indicated that the mice transplanted with iPSCs have a much higher rate of tumorigenicity than with ESCs.  
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The risks of iPSC tumorigenicity have been widely concerned over the past several years. In the study in 2009, Yamakana found out that, among the 55 mice who has been transplanted with iPS cell clones, 46 mice died or became weak within 9 weeks because of tumors. Whereas in contrast group, the number of the tumor-showing mice transplanted with ES cell clones was only 3 among 34<a class="quote">[4]</a>. This result indicated that the mice transplanted with iPSCs have a much higher rate of tumorigenicity than with ESCs.  
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<U><EM>- The "fantastic four"are double-edged swords:</EM></U> In the initial study in 2006, Yamanaka has pointed out that among the four transcriptional factors he used, two (Oct-4 and Myc) were oncogenes<a class="quote">[3]</a>. This led to the result that the iPSCs with the four exogenetic oncogenes were more prone to tumorigenesis. However, subsequent studies successively substantiated that both the Oct-4 and Myc are not essentially required for cell self-renewal. For example, in making human iPS cells, Yu et al. used a different set of four factors (Oct-4, Sox-2, Nanog, and Lin-28) to induce pluripotent stem cells from human somatic cells. These results began to raise the scientists' hopes to find the better combination of the cocktails to induce the safer iPSC. However, it turned out to be wishful thinking.  
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<U><EM>- The "fantastic four"are double-edged swords:</EM></U> In the initial study in 2006, Yamanaka has pointed out that among the four transcriptional factors he used, two (Oct-4 and Myc) were oncogenes<a class="quote">[5]</a>. This led to the result that the iPSCs with the four exogenetic oncogenes were more prone to tumorigenesis. Scientists figured out that almost every reprogramming factors are oncogenes by definition. Their over-expression are associated with some types of cancer. Of particular importance is the MYC transcription factor, which has emerged as one of the fundamental genes shared by iPSCs and cancer. Ectopic activation of OCT4 in somatic cells, induces dysplastic development and features of malignancy. NANOG has a role in the self renewal of CD24+ cancer stem cells in hepatocellular carcinoma. SOX2 has been shown to drive cancer-cell survival and oncogenic fate in several cancer types, including squamous cell carcinomas of the lung and esophagus. Klf-4 has been reported to promote DNA repair checkpoint uncoupling and cellular proliferation in breast cancers by p53 suppression<a class="quote">[6]</a>.  
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Scientists figure out that whatever the combination is, almost every inducing/reprogramming factors remaining in the cocktail are oncogenes by definition. Their over-expression has be associated with some forms of cancer. Of particular importance is the MYC transcription factor, which has emerged as one of the fundamental genes shared by iPSCs and cancer. Ectopic activation of OCT4 in somatic cells, induces dysplastic development and features of malignancy. NANOG has a role in the self renewal of CD24+ cancer stem cells in hepatocellular carcinoma. SOX2 has been shown to drive cancer-cell survival and oncogenic fate in several cancer types, including squamous cell carcinomas of the lung and esophagus. Klf-4 has been reported to promote DNA repair checkpoint uncoupling and cellular proliferation in breast cancers by p53 suppression<a class="quote">[7]</a>.  
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<U><EM>- Risks from delivery methods:</EM></U> Compared to ESCs, iPSCs are exposed to several factors that could cause oncogenic transformation, such as genomic insertion of reprogramming vectors, over expression of oncogenic transcription factors and a global hypomethylation resembling that seen in cancers<a class="quote">[6]</a>.  
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<U><EM>- Risks from delivery methods:</EM></U> Compared to ESCs, iPSCs are exposed to a number of factors that could promote oncogenic transformation, such as genomic insertion of reprogramming vectors, over expression of oncogenic transcription factors and a global hypomethylation resembling that seen in cancers<a class="quote">[7]</a>.
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Methods of diminishing the tumorigenic risks of iPSCs have mainly focused on a variety of gene delivery vectors that minimize genomic disruption. These strategies can be generally divided into two categories: integrating vectors that can be excised from the host genome and non-integrating vectors. However, all these methods can not escape their shortcomings of low transduction efficiency, or even bring about new risks. This summer, as a group of young pre-scientists, we came up with a new strategy to try to minimize this potential problem. </p>
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Methods of diminishing the tumorigenic transformation of iPSCs have mainly focused on a variety of gene delivery vectors that minimize genomic disruption. These strategies can be generally divided into two categories: integrating vectors that can be excised from the host genome and non-integrating vectors. However, all methods can not escape their shortcomings of low transduction efficiency, or even bring about new risks. For example, piggyBac transposition carries the risk of uncontrolled cycles of excision and integration, increasing the possibility of nonconservative deletions within coding regions of the genome. standard non-integrating strategies such as using adenoviruses suffer from extremely low transduction efficiencies (0.001%). In addition, considerable technical skills are required to carry out this type of reprogramming, and only a handful of centers have been able to successfully apply these strategies.  Here is a table which concludes the oncogenic risks associated with methods of inducing pluripotency in somatic cells<a class="quote">[7]</a>.
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<table width="536">
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<caption>Table 1 Oncogenic risks associated with methods of inducing pluripotency in somatic cells</caption>
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<th scope="col">Method of induction</th>
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<th scope="col">Strengths</th>
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<th scope="col">Weaknesses</th>
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<td>Lentiviral vector</td>
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<td>Robust reprogramming efficiency</td>
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<td>Genomic integration, reactivation of integrated transgenes</td>
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<tr>
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<td>Cre recombinase</td>
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<td>Little genomic disruption</td>
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<td>Low transduction efficiency, integration of LoxP sites into host genome</td>
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<tr>
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<td>PiggyBac transposition</td>
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<td>Minimal risk of genomic disruption</td>
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<td>Low transduction efficiency, risk of uncontrolled rounds of excision and integration</td>
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<tr>
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<td>Adenoviral vector </td>
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<td>Low risk of genomic integration</td>
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<td>Low transduction efficiency, limited transgene expression</td>
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<tr>
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<td>Plasmid transfection</td>
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<td>Minimal risk of genomic disruption</td>
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<td>Very low transduction efficiency typically requires use of oncogenes such as the SV40LT antigen for successful induction of pluripotency</td>
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<tr>
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<td>Minicircle</td>
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<td>Minimal risk of genomic disruption</td>
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<td>Low transduction efficiency</td>
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<tr>
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<td>Sendai virus</td>
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<td>Minimal risk of genomic integration ,relatively high transduction efficiency</td>
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<td>Risk of continuous replication of viral vector in cytoplasm, leading to aberrant silencing of pluripotency transgenes</td>
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<td>Synthetic mRNA</td>
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<td>No risk of genomic integration, ability to control transgene expression</td>
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<td>Variable transduction efficiencies, high technical expertise required</td>
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<td>Protein transduction</td>
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<td>No risk of genomic integration, ability to control transgene expression</td>
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<td>Very low transduction efficiency, labor intensive</td>
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<td>microRNA transfection</td>
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<td>No risk of genomic integration</td>
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<td>Low reprogramming efficiency</td>
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<td>Small molecules</td>
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<td>No risk of genomic integration</td>
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<td>Variable off-target effects</td>
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From the table above, we can generally conclude that these promising strategies for teratoma prevention mostly improve the safety of iPSC generation at the expense of efficiency, which is still another remaining challenge in iPSC technology.
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In summary, it wouldn't be more perfect if scientists found a method which guaranteed both the safety and efficiency in iPSCs technology. Just as Andrew S Lee wrote on Nature Medicine, "Ideally, the most stringent safety regimes would utilize a flexible, combinatorial approach that may require tailoring for specific PSC lines or graft types. Should these techniques fail to adequately remove enough residual PSCs, retrospective tumor treatments may also be used, including oncologic chemotherapy, radiation and surgery or the incorporation of suicide ablation genes<a class="quote">[7]</a>." Admittedly, just as the saying goes, "You can't have your cake and eat it!" With our knowledge of iPSC biology, it is not likable that such a perfect regime would emerge in several coming years. However, as a group of young pre-scientists like us, maybe, it is our time to look into this problem and try to figure it out in another way.
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<h1>microRNA Silencing</h1>
<h1>microRNA Silencing</h1>
<p>
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MicroRNAs are short 19-22nt RNAs that function as negative regulators of gene expression. Found in all animal and plant cells, as well as in viral genome, microRNAs regulate gene expression by binding to a short 6 nt region within the 3'UTR of their target mRNAs. In human cells, more than 1000 microRNAs have been described and nearly 50% of human mRNAs are predicted to be microRNA targets. Hence, microRNAs are one of the most regulatory elements in mammals.
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MicroRNA is a short 19-22nt RNA that functions as negative regulator of gene expression. By binding to a complementary target located at the 3’UTR of gene, it either triggers degradation of the whole mRNA in complete match or just blocks down protein translation when incomplete matching. There are more than 1000 kinds of microRNAs which are predicted to regulate approximately 50% of gene expression in human cells.<a class="quote">[7]</a>
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<h2>biogenesis and functioning of microRNAs</h2>
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<h2>biogenesis of microRNAs</h2>
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MicroRNAs can regulate gene expression and control many important process including development, differentiation, apoptosis and proliferation. An microRNA gene is transcribed by RNA polymerase II and becomes primary miRNA(pri-miRNA). Then, the RNase III endonuclease Drosha and the double-stranded RNA-binding domain (dsRBD) protein DGCR8/Pasha cleave the pri-miRNA to produce a 2-nt 3 overhang containing the ∼70-nt precursor miRNA (pre-miRNA) in the nucleus. Next, exportin-5 transports the pre-miRNA into the cytoplasm, where it is cleaved by another RNase III endonuclease, Dicer, together with the dsRBD protein TRBP/Loquacious. One strand of each double-stranded RNA is degraded and the other strand can target mRNA that contains the complementary sequence. Associated with other proteins, the microRNA-protein complex prevent gene expression either by degrading the target microRNA or by blocking its translation.
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MicroRNAs are mostly located in introns and transcribed by PolII before splicing. The transcribed pri-miRNA is then bound by double-stranded RNA-binding protein and cut by RNase III Drosha. A 70nt hairpin pre-miRNA is thus produced and transported outside the nucleus with the assistance of Exportin 5. After that, another RNaseIII Dicer cleave the pre-miRNA to generate mature microRNA duplex. One strand is incorporated into the RNA-induced silencing complex (RISC) and the other strand is degraded. When the incorporated single strand RNA finds its target, the mRNA will be degraded. <a class="quote">[8]</a><a class="quote">[9]</a></p>
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<img class="fig_img" width="700px" src=" https://static.igem.org/mediawiki/2013/archive/0/03/20130927144735%21Background-miRNA.png      " />
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<p class="des" style="margin-top:0px;width:700px"><strong>Figure 4.</strong>  Principle of microRNA      </p>
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<h2>liver-specific microRNA-122</h2>
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<h2>liver-specific miR-122</h2>
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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 microRNAs. Two studies could show that miR-122 appears to suppress 100–200 genes in liver tissue as demonstrated in mice.
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miR-122 targets the 3'UTR of the mRNAs of cytoplasmic polyadenylation element bindingprotein (CPEB), hemochromatosis (Hfe), hemojuverin(Hjv), disintegrin, and metalloprotease family 10(ADAM10) and represses their translation. miR-122 activates the translation of p53 mRNA through thesuppression of CPEB and participates in cellular senescence. Through the inhibition of Hfe and Hjv, miR-122 participates in iron metabolism. MiR-122 can also positively regulated lipid metabolism through the reduction of the mRNAs of lipid-associated proteins, and that inhibition of miR-122 expression attenuated liver steatosis in high-fat-fed mice, suggesting that miR-122 may be an attractive therapeutic target for metabolic diseases. Although Li et al. have suggested that hepatocyte nuclear factor 4 alpha (HNF4A) positively regulates the expression of miR-122, the details on the tissue specificity of miR-122 expression have not been fully elucidated yet.
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First attempts to use miR-122 as a therapeutic drug target have been already made by developing antagomirs against miR-122 and to test them as a putative treatment option for hepatitis C or for diseases associated with an aberrant cholesterol homeostasis.
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MicroRNA-122(miR-122) is most abundantly expressed in normal liver cells instead of liver cancer cells or other kinds of tissue cells. It accounts for approximately 70%of all the microRNAs in normal liver cells.  The detailed regulatory network and the reason for its specificity is still in researches, but we know that miR-122 can target nearly 300 genes including Hfe, CPEB, ADAM10 and indirectly regulates downstream genes including p53. For functional tests, it is believed that miR-122 can regulate lipid metabolism and assist iron metabolism as well as HCV infection. Knocking down the endogenous level of miR-122 by antisense antagomirs will not interfere normal liver functions as indicated by clinical trials on the treatment of cholesterol metabolism and HCV infection. microRNA-122(miR-122) is most abundantly expressed in normal liver cells instead of liver cancer cells or other kinds of tissue cells. It accounts for approximately 70%of all the microRNAs in normal liver cells.  The detailed regulatory network and the reason for its specificity is still in researches, but we know that miR-122 can target nearly 300 genes including Hfe, CPEB, ADAM10 and indirectly regulates downstream genes including p53. For functional tests, it is believed that miR-122 can regulate lipid metabolism and assist iron metabolism as well as HCV infection. Knocking down the endogenous level of miR-122 by antisense antagomirs will not interfere normal liver functions as indicated by clinical trials on the treatment of cholesterol metabolism and HCV infection.  
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<h1>From iPSC to Hepatocytes</h1>
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<h1>iPSC-derived hepatocytes</h1>
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Hepatocytes have been differentiated from various kinds of cell sources, including mesenchymal, fibroblast, and embryonic stem cells. iPS-derived hepatocytes have been generated from a variety of species including mouse, human and pig. These iPS cells can be expanded and directly differentiated into hepatocytes in vitro and are capable of many hepatic functions like albumin secretion. Also human iPS-derived hepatocytes exhibit key morphological features of differentiated hepatoctes. One of the promising applications of iPS-derived hepatocytes will be to study inherited metabolic disorders of the liver such as progressive familial gereditary cholestasis, a1-antitrypsin deficiency, glycogen storage disease type 1a, familial hypercholesterolemia, hereditary tyrosinemia and Crigler–Najjar syndrome.  
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Hepatocytes are always in need for tissue transplant and hepatoxity screening. Due to the limitation of tissue origin and the difficulties for isolation and maintains, iPSC-derived hepatocytes provide us a new way to generate hepatocytes for clinical use and study tossie origin  and metabolism in patient with inherent diseases. <a class="quote">[10]</a>.  
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In recent studies, iPS-derived hepatocytes have been tested to determine the potential for cell replacement therapy and can be applied to produce metabolically competent hepatic cell lines. It can circumvent the drawbacks of primary human hepatocytes of the phenotypic instability over time, scarce tissue origin and the high batch-to-batch functional variability. What's more, the function of hepatocytes in human body differs from region to region of a liver because one cell does not hold all the enzymes responsible for the complex metabolism within human body. Previously set up liver-derived cancer cell line have been transfected to express metabolic-related genes. However, engineered liver cancer cell lines are tumor origin and bring in the concerns that they could not represent a normal liver. By using iPS-derived hepatocytes, we can integrate gene circuits to express metabolic enzymes to a normal level and respond to environmental changes and better mimic how a naturally hepatocytes works.
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In recent study, iPSC-derived liver with certain metabolic function has been generated and tested for cell replacement therapy. It can circum the drawback of phenotypic instability, scarce tissue origin and damage to normal tissue. iPSC-derived hepatocytes can better mimics normal metabolic pathways than cancer cell line due to purer genetic background.</p>
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<img class="fig_img" width="760px" src="    https://static.igem.org/mediawiki/2013/c/cd/SYSU-Background.png    " />
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<p class="des" style="margin-top:0px;width:700px"><strong>Figure 5.</strong>    Application of iPSC-derived hepatocytes     </p>
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<h2>References</h2>
<h2>References</h2>
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<p><a class="references">[1]</a>The strategy of genes. CH Waddington& H Kacser. -1957</p>
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<p><a class="references">[1]</a>Scientific Background: Mature cells can be reprogrammed to become pluripotent. Nobelprize.org. Nobel Media 2012</p>
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<p><a class="references">[2]</a>Gurdon JB (1962). Developmental Capacity of Nuclei Taken From IntestinalEpithelium Cells of Feeding Tadpoles. J Embryol Exp Morph 10: 622‐640.</p>
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<p><a class="references">[2]</a>Shinya Yamanaka, Cell Stem Cell ,10, 6,(2012)</p>
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<p><a class="references">[3]</a>Takahashi, K. & Yamanaka, Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. S. Cell 126, 663–676 (2006).</p>
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<p><a class="references">[3]</a>SHI V. LIU, Stem cell development. 17,391(2008)</p>
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<p><a class="references">[4]</a>James A. Thomson et al, Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells. Science 21 December 2007: Vol. 318 no. 5858 pp. 1917-1920 </p>
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<p><a class="references">[4]</a>Shinya Yamanaka et al. Natue biotechnology, 27, 743(2009)</p>
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<p><a class="references">[5]</a>Scientific Background: Mature cells can be reprogrammed to become pluripotent. Nobelprize.org. Nobel Media 2012 </p>
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<p><a class="references">[5]</a>Takahashi, K. & Yamanaka, Cell ,126, 663,(2006) </p>
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<p><a class="references">[6]</a>Shinya Yamanaka, Induced Pluripotent Stem Cells: Past, Present, and Future. Cell Stem Cell 10, June 14, 2012</p>
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<p><a class="references">[6]</a>Andrew S Lee et al.. Nature Medicine, 19, 998(2013)</p>
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<p><a class="references">[7]</a>Andrew S Lee et al. Tumorigenicity as a clinical hurdle for pluripotent stem cell therapies. Nature Medicine, valume 19, august 2013;</p>
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<p><a class="references">[7]</a>Xie X, et al,Nature, 434,7031,( 2005)</p>
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<p><a class="references">[8]</a>SHI V. LIU, iPS Cells: A More Critical Review. Stem cell development. 17:391–397 (2008)</p>
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<p><a class="references">[8]</a>Han J, Lee Y, Yeom K H, et al. ,Genes & development, 18,24,(2004)</p>
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<p><a class="references">[9]</a>Tetsuya Ishii,1,* Renee A. Reijo Pera,2 and Henry T. Greely3, Ethical and Legal Issues Arising in Research on Inducing Human Germ Cells from Pluripotent Stem Cells. Cell Stem Cell 13, August 1, 2013</p>
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<p><a class="references">[9]</a>Chendrimada T P, Gregory R I, Kumaraswamy E, et al. Nature, 436,7051,(2005)</p>
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<p><a class="references">[10]</a>Martin F Pera & Kouichi Hasegawa, Simpler and safer cell reprogramming, Nature biotechnology, volume 26, january 2008.</p>
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<p><a class="references">[10]</a>Rao M S, Sasikala M, Reddy D N,19,22 ( 2013)</p>
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<p><a class="references">[11]</a>Shinya Yamanaka et al. Variation in the safety of induced pluripotent stem cell lines, Natue biothchnology, volume 27, august 2009.</p>
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<p><a class="references">[12]</a>Shinya Yamanaka et al. Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors, Cell, 30 November 2007, Pages 861–872</p>
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<p><a class="references">[13]</a>Gunnar Hargusa et al. Differentiated Parkinson patient-derived induced pluripotent stem cells grow in the adult rodent brain and reduce motor asymmetry in Parkinsonian rats, PNAS, September 7, 2010</p>  
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<p><a class="references">[14]</a>Xie X, Lu J, Kulbokas E J, et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals[J]. Nature, 2005, 434(7031): 338-345.</p>  
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<p><a class="references">[15]</a>Han J, Lee Y, Yeom K H, et al. The Drosha-DGCR8 complex in primary microRNA processing[J]. Genes & development, 2004, 18(24): 3016-3027.</p>  
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<p><a class="references">[16]</a>Chendrimada T P, Gregory R I, Kumaraswamy E, et al. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing[J]. Nature, 2005, 436(7051): 740-744.</p>
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<p><a class="references">[17]</aEsau C, Davis S, Murray S F, et al. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting[J]. Cell metabolism, 2006, 3(2): 87-98.</p>  
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<p><a class="references">[18]</a>Burns D M, D’Ambrogio A, Nottrott S, et al. CPEB and two poly (A) polymerases control miR-122 stability and p53 mRNA translation[J]. Nature, 2011, 473(7345): 105-108.</p>
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<p><a class="references">[19]</a>Rao M S, Sasikala M, Reddy D N. Thinking outside the liver: Induced pluripotent stem cells for hepatic applications[J]. World J Gastroenterol, 2013, 19(22): 3385-3396.</p>
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<p><a class="references">[20]</a>Fukuhara T, Matsuura Y. Role of miR-122 and lipid metabolism in HCV infection[J]. Journal of gastroenterology, 2012: 1-8.</p>
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<p><a class="references">[21]</a>Bushati N, Cohen S M. microRNA functions[J]. Annu. Rev. Cell Dev. Biol., 2007, 23: 175-205.</p>
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Latest revision as of 03:59, 29 October 2013

ipsc

Project/Background

iPSCs

What is iPSCs?

Life there and back again

In the past century, scientists always believed that the life's one-way journey also applied to cells: Once a cell has developed into a specialized cell, it would be locked at that situation, unable to return back to pluripotent stem cell.

However, this prevalent view was radically overturned in 2006, when Shinya Yamanaka, a Japanese scientist who afterward shared the 2012 Nobel Prize in Physiology or Medicine with John B. Gurdon[1], proved that introduction of four transcription factors into a differentiated cell was sufficient to return the cell into a pluripotent situation. In his experiment, what Yamakana did was introducing four genes encoding the transcription factors (Myc, Oct3/4, Sox2 and Klf4), which were selected to reinstate pluripotency in somatic cells to skin fibroblasts. These synthetical new stem cells were thereafter named by their Japanese father as iPSCs (induced pluripotent stem cells). A year later, using the same four transcription factors in the 2006 paper, Yamanka's group successfully produced human iPS cells.

A technology with many possibilities

The groundbreaking work that Yamakana and his group did in 2006 truly opened up a completely new research field to this world. It was a paradigm-shifting fundamental breakthrough, as it firstly demonstrated that an differentiated somatic cell could be reprogrammed to be pluripotent stem cell again. iPSCs technology, a new technology with many possibilities, attracts scientists and researchers all over the world, mainly for its three unique superiorities:

- No strong immunological reaction: Since iPS cells can be cultured from the patient's own cells, it is not quite possible to lead to immunological reaction when directionally differentiated iPSCs are transplanted after in vitro culture. While in 2011 several studies argued the weak immune reaction to transgene-free iPSCs, these arguments were subsided later by other scientists and Yamanaka himself, pointing out that "the most prominent study that reported the immunogenicity of the cells examined undifferentiated iPSCs, which will never be used in cell transplantation therapy"[2].

- "Thank god we don't need embryos anymore!": Simultaneously, the technology of iPSC was also hailed by many commentaries for it solved the ethical problems in stem cell research field. In the past, stem cell research relied heavily of embryonic stem cells harvested from embryos. Human embryos are not easy to come by, and many people consider research involving use of human embryonic stem cells to be ethically questionable. With no further evidence, iPSC technology not only “breaks the ethical barrier of relying on using eggs or earlier embryos for deriving stem cells, but also leads to a convenient way of obtaining patient-specific stem cells”[3].

- Wide application in different fields: Nowadays, scientists are making progress in applying iPSCs in many fields. One of the applications - which has already become reality - is to use iPS cells in both analysing disease mechanisms and investigating potential new treatments. In the future scientists hope to be able to use iPS cells to culture cells that can be transplanted into the body and replace diseased cells.

These advances above together made the iPSC to be the "star cell" which offers immense potential as a source for regenerative therapies. However, the intrinsic qualities of self renewal and pluripotency that make these cells so promising are also causing equally fundamental tumorigenic risks, and the intrinsic shortcomings of the current methods of inducing pluripotency even pose more uncontrollable risks on that. High rates of tumorigenicity has become a most crucial hurdle for clinical implementation of iPSC technology.

Challenges

Tumorigenicity as a clinical hurdle

The risks of iPSC tumorigenicity have been widely concerned over the past several years. In the study in 2009, Yamakana found out that, among the 55 mice who has been transplanted with iPS cell clones, 46 mice died or became weak within 9 weeks because of tumors. Whereas in contrast group, the number of the tumor-showing mice transplanted with ES cell clones was only 3 among 34[4]. This result indicated that the mice transplanted with iPSCs have a much higher rate of tumorigenicity than with ESCs.

- The "fantastic four"are double-edged swords: In the initial study in 2006, Yamanaka has pointed out that among the four transcriptional factors he used, two (Oct-4 and Myc) were oncogenes[5]. This led to the result that the iPSCs with the four exogenetic oncogenes were more prone to tumorigenesis. Scientists figured out that almost every reprogramming factors are oncogenes by definition. Their over-expression are associated with some types of cancer. Of particular importance is the MYC transcription factor, which has emerged as one of the fundamental genes shared by iPSCs and cancer. Ectopic activation of OCT4 in somatic cells, induces dysplastic development and features of malignancy. NANOG has a role in the self renewal of CD24+ cancer stem cells in hepatocellular carcinoma. SOX2 has been shown to drive cancer-cell survival and oncogenic fate in several cancer types, including squamous cell carcinomas of the lung and esophagus. Klf-4 has been reported to promote DNA repair checkpoint uncoupling and cellular proliferation in breast cancers by p53 suppression[6].

- Risks from delivery methods: Compared to ESCs, iPSCs are exposed to several factors that could cause oncogenic transformation, such as genomic insertion of reprogramming vectors, over expression of oncogenic transcription factors and a global hypomethylation resembling that seen in cancers[6].

Methods of diminishing the tumorigenic risks of iPSCs have mainly focused on a variety of gene delivery vectors that minimize genomic disruption. These strategies can be generally divided into two categories: integrating vectors that can be excised from the host genome and non-integrating vectors. However, all these methods can not escape their shortcomings of low transduction efficiency, or even bring about new risks. This summer, as a group of young pre-scientists, we came up with a new strategy to try to minimize this potential problem.

microRNA Silencing

MicroRNA is a short 19-22nt RNA that functions as negative regulator of gene expression. By binding to a complementary target located at the 3’UTR of gene, it either triggers degradation of the whole mRNA in complete match or just blocks down protein translation when incomplete matching. There are more than 1000 kinds of microRNAs which are predicted to regulate approximately 50% of gene expression in human cells.[7]

biogenesis of microRNAs

MicroRNAs are mostly located in introns and transcribed by PolII before splicing. The transcribed pri-miRNA is then bound by double-stranded RNA-binding protein and cut by RNase III Drosha. A 70nt hairpin pre-miRNA is thus produced and transported outside the nucleus with the assistance of Exportin 5. After that, another RNaseIII Dicer cleave the pre-miRNA to generate mature microRNA duplex. One strand is incorporated into the RNA-induced silencing complex (RISC) and the other strand is degraded. When the incorporated single strand RNA finds its target, the mRNA will be degraded. [8][9]

Figure 4. Principle of microRNA

liver-specific miR-122

MicroRNA-122(miR-122) is most abundantly expressed in normal liver cells instead of liver cancer cells or other kinds of tissue cells. It accounts for approximately 70%of all the microRNAs in normal liver cells. The detailed regulatory network and the reason for its specificity is still in researches, but we know that miR-122 can target nearly 300 genes including Hfe, CPEB, ADAM10 and indirectly regulates downstream genes including p53. For functional tests, it is believed that miR-122 can regulate lipid metabolism and assist iron metabolism as well as HCV infection. Knocking down the endogenous level of miR-122 by antisense antagomirs will not interfere normal liver functions as indicated by clinical trials on the treatment of cholesterol metabolism and HCV infection. microRNA-122(miR-122) is most abundantly expressed in normal liver cells instead of liver cancer cells or other kinds of tissue cells. It accounts for approximately 70%of all the microRNAs in normal liver cells. The detailed regulatory network and the reason for its specificity is still in researches, but we know that miR-122 can target nearly 300 genes including Hfe, CPEB, ADAM10 and indirectly regulates downstream genes including p53. For functional tests, it is believed that miR-122 can regulate lipid metabolism and assist iron metabolism as well as HCV infection. Knocking down the endogenous level of miR-122 by antisense antagomirs will not interfere normal liver functions as indicated by clinical trials on the treatment of cholesterol metabolism and HCV infection.

iPSC-derived hepatocytes

Hepatocytes are always in need for tissue transplant and hepatoxity screening. Due to the limitation of tissue origin and the difficulties for isolation and maintains, iPSC-derived hepatocytes provide us a new way to generate hepatocytes for clinical use and study tossie origin and metabolism in patient with inherent diseases. [10].

In recent study, iPSC-derived liver with certain metabolic function has been generated and tested for cell replacement therapy. It can circum the drawback of phenotypic instability, scarce tissue origin and damage to normal tissue. iPSC-derived hepatocytes can better mimics normal metabolic pathways than cancer cell line due to purer genetic background.

Figure 5. Application of iPSC-derived hepatocytes

References

[1]Scientific Background: Mature cells can be reprogrammed to become pluripotent. Nobelprize.org. Nobel Media 2012

[2]Shinya Yamanaka, Cell Stem Cell ,10, 6,(2012)

[3]SHI V. LIU, Stem cell development. 17,391(2008)

[4]Shinya Yamanaka et al. Natue biotechnology, 27, 743(2009)

[5]Takahashi, K. & Yamanaka, Cell ,126, 663,(2006)

[6]Andrew S Lee et al.. Nature Medicine, 19, 998(2013)

[7]Xie X, et al,Nature, 434,7031,( 2005)

[8]Han J, Lee Y, Yeom K H, et al. ,Genes & development, 18,24,(2004)

[9]Chendrimada T P, Gregory R I, Kumaraswamy E, et al. Nature, 436,7051,(2005)

[10]Rao M S, Sasikala M, Reddy D N,19,22 ( 2013)

Sun Yat-Sen University, Guangzhou, China

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