Induced pluripotent stem cell

Induced pluripotent stem cells,[1] commonly abbreviated as iPS cells or iPSCs are a type of pluripotent stem cell artificially derived from a non-pluripotent cell, typically an adult somatic cell, by inducing a "forced" expression of specific genes.

Induced Pluripotent Stem Cells are similar to natural pluripotent stem cells, such as embryonic stem (ES) cells, in many respects, such as the expression of certain stem cell genes and proteins, chromatin methylation patterns, doubling time, embryoid body formation, teratoma formation, viable chimera formation, and potency and differentiability, but the full extent of their relation to natural pluripotent stem cells is still being assessed.[2]

iPSCs were first produced in 2006 from mouse cells and in 2007 from human cells. This has been cited as an important advance in stem cell research, as it may allow researchers to obtain pluripotent stem cells, which are important in research and potentially have therapeutic uses, without the controversial use of embryos. Because iPSCs are developed from a patient's own somatic cells, it was believed that treatment of iPSCs would avoid any immunogenic responses; however, Zhao et al. have challenged this assumption.[3]

Depending on the methods used, reprogramming of adult cells to obtain iPSCs may pose significant risks that could limit its use in humans. For example, if viruses are used to genomically alter the cells, the expression of cancer-causing genes or oncogenes may potentially be triggered. In February 2008, in ground-breaking findings published in the journal Cell, scientists announced the discovery of a technique that could remove oncogenes after the induction of pluripotency, thereby increasing the potential use of iPS cells in human diseases.[4] In April 2009, it was demonstrated that generation of iPS cells is possible without any genetic alteration of the adult cell: a repeated treatment of the cells with certain proteins channeled into the cells via poly-arginine anchors was sufficient to induce pluripotency.[5] The acronym given for those iPSCs is piPSCs (protein-induced pluripotent stem cells).

Contents

Production of iPSCs

iPS cells are typically derived by transfection of certain stem cell-associated genes into non-pluripotent cells (although this technique is becoming less popular since it is known to be prone to cancer formation), such as adult fibroblasts. Transfection is typically achieved through viral vectors, such as retroviruses. Transfected genes include the master transcriptional regulators Oct-3/4 (Pou5f1) and Sox2, although it is suggested that other genes enhance the efficiency of induction. After 3–4 weeks, small numbers of transfected cells begin to become morphologically and biochemically similar to pluripotent stem cells, and are typically isolated through morphological selection, doubling time, or through a reporter gene and antibiotic selection.

First generation

Induced pluripotent stem cells were first generated by Shinya Yamanaka's team at Kyoto University, Japan in 2006. Yamanaka used genes that had been identified as particularly important in embryonic stem cells (ESCs), and used retroviruses to transduce mouse fibroblasts with a selection of those genes. Eventually, four key pluripotency genes essential for the production of pluripotent stem cells were isolated; Oct-3/4, SOX2, c-Myc, and Klf4. Cells were isolated by antibiotic selection of Fbx15+ cells. However, this iPS cell line showed DNA methylation errors compared to original patterns in ESC lines and failed to produce viable chimeras if injected into developing embryos.

Second generation in mice

In June 2007, the same group published a breakthrough study along with two other independent research groups from Harvard, MIT, and the University of California, Los Angeles, showing successful reprogramming of mouse fibroblasts into iPS cells and even producing viable chimera. These cell lines were also derived from mouse fibroblasts by retroviral mediated reactivation of the same four endogenous pluripotent factors, but the researchers now selected a different marker for detection. Instead of Fbx15, they used Nanog which is an important gene in ESCs. DNA methylation patterns and production of viable chimeras (and thereby contributing to subsequent germ-line production) indicated that Nanog is a major determinant of cellular pluripotency.[6][7][8][9][10]

Unfortunately, one of the four genes used (namely, c-Myc) is oncogenic, and 20% of the chimeric mice developed cancer. In a later study, Yamanaka reported that one can create iPSCs even without c-Myc. The process takes longer and is not as efficient, but the resulting chimeras didn't develop cancer.[11]

Two-fathered mice

Reproductive scientists in University of Texas MD Anderson Cancer Center have created mice with nuclear DNA (nDNA) solely from two fathers, using iPS technology.[12][13] Foetal fibroblasts from one father (XY) were cultivated and one percent of the resultant cells had spontaneously lost a Y-chromosome; like an individual with Turner Syndrome (X0).[14] These cells were injected in female blastocysts (XX), which gestated in surrogate mothers to form female chimeras (X0/XX). When these mated with male mice (XY). Some of the offspring had nDNA from the original father and also from the mated male but not from the female blastocysts or the surrogate mother. Both male and female two-fathered mice were viable.

Human induced pluripotent stem cells

In November 2007, a milestone was achieved[1][15] by creating iPSCs from adult human cells; two independent research teams' studies were released - one in Science by James Thomson at University of Wisconsin–Madison[16] and another in Cell by Shinya Yamanaka and colleagues at Kyoto University, Japan.[17] With the same principle used earlier in mouse models, Yamanaka had successfully transformed human fibroblasts into pluripotent stem cells using the same four pivotal genes: Oct3/4, Sox2, Klf4, and c-Myc with a retroviral system. Thomson and colleagues used OCT4, SOX2, NANOG, and a different gene LIN28 using a lentiviral system.

Limitations of the transcription factor approach

Although the traditional method using transcription factors such as Oct3/4, Sox2, c-Myc, etc. pioneered by Yamanaka and Thompson was good proof of concept that somatic cells can be reprogrammed to iPS cells, there are still many key challenges for this method to overcome:

  1. Throughput: the throughput of successfully reprogrammed cells has been incredibly low. For example, the rate at which somatic cells were reprogrammed into iPS cells in the Yamanaka mouse study was .01-.1%.[6] The low efficiency rate may reflect the need for precise timing, balance, and absolute levels of expression of the reprogramming genes. It may also suggest a need for rare genetic and/or epigenetic changes in the original somatic cell population or in the prolonged culture.
  2. Genomic Insertion: genomic integration of the transcription factors limits the utility of the transcription factor approach because of the risk of mutations being inserted into the target cell’s genome.[18] A common strategy for avoiding genomic insertion has been to use a different vector for input. plasmids , adenovirus es, and transposon vectors have all been explored, but these often come with the tradeoff of lower throughput.[19][20][21]
  3. Tumors: another main challenge was mentioned above—some of the reprogramming factors are oncogenes that bring on a potential tumor risk. Inactivation or deletion of the tumor suppressor p53, which is the master regulator of cancer, significantly increases reprogramming efficiency.[22] Thus there seems to be a tradeoff between reprogramming efficiency and tumor generation.
  4. Incomplete reprogramming: reprogramming also faces the challenge of completeness. This is particularly challenging because the genome-wide epigenetic code must be reformatted to that of the target cell type in order to fully reprogram a cell. However, three separate groups were able to find mouse embryonic fibroblast (MEF)-derived iPS cells that could be injected into tetraploid blastocysts and resulted in the live birth of mice derived entirely from iPS cells, thus ending the debate over the equivalence of embryonic stem cells (ESCs) and iPS with regard to pluripotency.[23] However, some of the other techniques profiled below demonstrated limited or incomplete equivalent to ESCs.

The table at right summarizes the key strategies and techniques used to develop iPS cells over the past half-decade. Rows of similar colors represents studies that used similar strategies for reprogramming.

Mimicking transcription factors with small compounds

One of the main strategies for avoiding problems (1) and (2) has been to use small compounds that can mimic the effects of transcription factors. These molecule compounds can compensate for a reprogramming factor that does not effectively target the genome or fails at reprogramming for another reason; thus they raise reprogramming efficiency. They also avoid the problem of genomic integration, which in some cases contributes to tumor genesis. Key studies using such strategy were conducted in 2008. Melton et al. studied the effects of histone deacetylase (HDAC) inhibitor valproic acid. They found that it increased reprogramming efficiency 100-fold (compared to Yamanaka’s traditional transcription factor method).[24] The researchers proposed that this compound was mimicking the signaling that is usually caused by the transcription factor c-Myc. A similar type of compensation mechanism was proposed to mimic the effects of Sox2. In 2008, Ding et al. used the inhibition of histone methyl transferase (HMT) with BIX-01294 in combination with the activation of calcium channels in the plasma membrane in order to increase reprogramming efficiency.[25] It is foreseeable that such experiments will continue to find small compounds that improve efficiency rates. Ultimately, the goal is to discover a cocktail of reprogramming factors and compounds that efficiently and reliably reprogram somatic cells to iPS cells.

Alternate vectors

Another key strategy for avoiding problems such as tumor genesis and low throughput has been to use alternate forms of vectors: adenovirus, plasmids, and naked DNA and/or protein compounds.

In 2008, Hochedlinger et al. used an adenovirus to transport the requisite four transcription factors into the DNA of skin and liver cells of mice, resulting in cells identical to ESCs. The adenovirus is unique from other vectors like viruses and retroviruses because it does not incorporate any of its own genes into the targeted host and avoids the potential for insertional mutagenesis.[26] More recently (in 2009), Freed et al. demonstrated successful reprogramming of human fibroblasts to iPS cells.[27] Another advantage of using adenoviruses is that they only need to present for a brief amount of time in order for effective reprogramming to take place.

Also in 2008, Yamanaka et al. once again made a huge contribution to the field of iPS cells with the finding that they could transfer the four necessary genes with a plasmid.[28] The Yamanaka group successfully reprogrammed mouse cells by transfection with two plasmid constructs carrying the reprogramming factors; the first plasmid expressed c-Myc, while the second expressed the other three factors (Oct4, Klf4, and Sox2). Although the plasmid methods avoid viruses, they still require cancer-promoting genes to accomplish reprogramming. The other main issue with these methods is that they tend to be much less efficient compared to retroviral methods. Furthermore, transfected plasmids have been shown to integrate into the host genome and therefore they still pose the risk of insertional mutagenesis. Because non-retroviral approaches have demonstrated such low efficiency levels, researchers have attempted to effectively rescue the technique with what is known as the piggyBac transposon system. The lifecycle of this system is shown below. Several studies have demonstrated that this system can effectively deliver the key reprogramming factors without leaving any footprint mutations in the host cell genome. As you can see in the figure, the piggyBac transposon system involves the re-excision of exogenous genes, and this is what prevents this method from causing issues like insertional mutagenesis

Drug-Like chemicals, recombinant proteins

In 2009, Ding and colleagues demonstrated a successful alternative to transcription factor reprogramming through the use of drug-like chemicals. This was the first method in human cells that was mechanism-specific for the reprogramming process. Ding tackled the problem of genomic insertion by using purified proteins to transform adult cells into embryonic-like cells.[29] Once his team successfully demonstrated this, they tackled the efficiency problem. Ding’s overall strategy involved biomimicry. He studied the naturally occurring process of MET (mesenchymal to epithelial cell transition), in which fibroblasts are pushed to a stem-cell like state. Ding first looked for drug-like molecules that inhibited compounds known to be involved in the MET process; these compounds included TGFb (transforming growth factor beta) and MEK (mitogen-activated protein kinase). Ding identified the most active molecules and then studied their effects on iPS creation when used singly or in combination. He concluded that there are two chemicals—ALK5 inhibitor SB431412 and MEK inhibitor PD0325901, which when used in combination are highly effective at promoting the transformation from fibroblast to iPS cell. Although this two-chemical technique bested the efficiency of the classical genetic method by 100fold, Ding sought to do better. He continued with the use of the biomimicry strategy, enlisting another natural pathway—the cell survival pathway. After screening several compounds that target this pathway, the team focused on a new compound called Thiazovivin. Using this protein with the two previous chemicals, the team beat the efficiency of the classic method by 200 fold. Furthermore, this method took only two weeks to complete reprogramming while the classic method took four weeks. Another advantage of Ding’s method was that it overcame the genetic insertion problem because the drug-like molecules were based on natural biological processes.

RNA molecules

Studies by Blelloch et al. in 2009 demonstrated that expression of ES cell-specific microRNA molecules (such as miR-291, miR-294 and miR-295) enhances the efficiency of induced pluripotency by acting downstream of c-Myc .[30] More recently (in April 2011), Morrisey et al. demonstrated another method using microRNA that improved the efficiency of reprogramming to a rate similar to that demonstrated by Ding. MicroRNAs are short RNA molecules that bind to complementary sequences on messenger RNA and block expression of a gene. Morrisey’s team worked on microRNAs in lung development, and hypothesized that their microRNAs perhaps blocked expression of repressors of Yamanaka’s four transcription factors.

Genes of induction

The generation of iPS cells is crucially dependent on the genes used for the induction.

Oct-3/4 and certain members of the Sox gene family (Sox1, Sox2, Sox3, and Sox15) have been identified as crucial transcriptional regulators involved in the induction process whose absence makes induction impossible. Additional genes, however, including certain members of the Klf family (Klf1, Klf2, Klf4, and Klf5), the Myc family (c-myc, L-myc, and N-myc), Nanog, and LIN28, have been identified to increase the induction efficiency.

An open future

The task of producing iPS cells continues to be challenging due to the five problems mentioned above. A key tradeoff to overcome is that between efficiency and genomic integration. Most methods that do not rely on the integration of transgenes are inefficient, while those that do rely on the integration of transgenes face the problems of incomplete reprogramming and tumor genesis. Of course there are a vast number of techniques and methods that have been attempted. Another large set of strategies is to perform a proteomic characterization of iPS cells. The Wu group at Stanford University has made significant headway with this strategy.[31] Further studies and new strategies should help us find optimal solutions to the five main challenges. An interesting experiment might attempt to combine the good of these strategies into an ultimately effective technique for reprogramming cells to iPS cells.

Identity

The generated iPSCs were remarkably similar to naturally-isolated pluripotent stem cells (such as mouse and human embryonic stem cells, mESCs and hESCs, respectively) in the following respects, thus confirming the identity, authenticity, and pluripotency of iPSCs to naturally-isolated pluripotent stem cells:

Safety for Regenerative Medicine

See also

References

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