STAP Cells: The Plot Thickens Even More


You might remember that Charles Vacanti and researchers at the RIKEN Institute in Japan reported a protocol for reprogramming mature mouse cells into pluripotent stem cells that could not only integrate into mouse embryos, but could also contribute to the formation of the placenta. To convert mature cells into pluripotent cells, Vacanti and others exposed the cells to slightly acidic conditions or other types of stressful conditions and the cells reverted to a pluripotent state.

Even though Vacanti and others published these results in the prestigious journal Nature, as other scientists tried to replicate the results in these papers, they found themselves growing more and more frustrated. Also, some gaffes with a few of the figures contributed to a kind of pall that has hung over this research in general.

The original makers of these cells, stress-acquired acquisition of pluripotency or STAP cells, have now made a detailed protocol of how they made their STAP cells publicly available at the Nature Protocol Exchange. Already. it is clear that a few things about the original paper are generating many questions.

First of all, Charles Vacanti’s name does not appear on the protocol. He was the corresponding author of the original paper. Therefore the absence of his name raises some eyebrows. Secondly, the authors seem to have backed off a few of their original claims.

For example one of the statements toward the beginning of the protocol says, “Despite its seeming simplicity, this procedure requires special care in cell handling and culture conditions, as well as in the choice of the starting cell population.” Whereas the original paper, on the first reading at least, seemed to convey that making STAP cells was fairly straightforward, this seems to no longer be the case, if the words of this protocol are taken at face value.

Also, the protocol notes that cultured cells do not work with their protocol. The authors write, “Primary cells should be used. We have found that it is difficult to reprogram mouse embryonic fibroblasts (MEF) that have been expanded in vitro, while fresh MEF are competent.”  This would probably explain inability of several well-regarded stem cell laboratories to recapitulate this work, since the majority of them probably used cultured cells. This, however, seems to contradict claims made in the original paper that multiple, distinct cell types could be converted into STAP cells.

Another clarification that the protocol provides that was not made clear in the original paper is that STAP cells and STAP stem cells are not the same thing. According to the authors, the protocol provided at Nature Protocol Exchange produces STAP cells, which have the capacity to contribute to the embryo and the placenta. On the other hand, STAP stem cells, are made from STAP cells by growing them in ACTH-containing medium on feeder cells, after which the cells are switched to ESC media with 20% Fetal Bovine Serum. STAP stem cells have lost the ability to contribute to extra-embryonic tissues.

Of even greater concern is a point raised by Paul Knoepfler at UC Davis. Knoepfler noticed that the original paper argued that some of their STAP cells were made from mature T cells. T cells rearrange the genes that encode the T cell receptor. If these mature T cells were used to make STAP cells, then they should have rearranged T cell receptor genes. The paper by Vacanti and others shows precisely that in a figure labeled 1i. However, in the protocol, the authors state that their STAP cells were NOT made from T-cells. In Knoepfler’s words: “On a simple level to me this new statement seems like a red flag.”

Other comments from Knoepfler’s blog noted that the protocol does not work on mice older than one week old. Indeed, the protocol itself clearly states that “Cells from mice older than one week showed very poor reprogramming efficiency under the current protocol. Cells from male animals showed higher efficiency than those from female.”  Thus the universe of cells that can be converted into STAP cells seems to have contracted by quite a bit.

From all this it seems very likely that the STAP paper will need to go through several corrections. Some think that the paper should be retracted altogether. I think I agree with Knoepfler and we should take a “wait and see” approach. If some scientists can get this protocol to work, then great. But even then, multiple corrections to the original paper will need to be submitted. Also, the usefulness of these procedure for regenerative medicine seems suspect, at least at the moment. The cells types that can be reprogrammed with this protocol are simply too few for practical use. Also, to date, we only have Vacanti’s word that this protocol works on human cells. Forgive me, but given the gaffes associated with this present paper, that’s not terribly reassuring.

Results of STAP Cell Paper Questioned


Reports of Stimulus-Triggered Acquisition of Pluripotency or STAP cells has rocked the stem cell world. If adult cells can be converted into pluripotent stem cells so easily, then perhaps personalized, custom stem cells for each patient are just around the corner.

However, the RIKEN institute, which was heavily involved in the research that brought STAP cells to the world has now opened an investigation into this research, since leading scientists have voiced discrepancies about some of the figures in the paper and others have failed to reproduce the results in the paper.

Last week, Friday (February 14, 2014, spokespersons for the RIKEN centre, which is in Kobe, Japan, announced that the institute is looking into alleged irregularities in the work of biologist Haruko Obokata, who works at the institution. Obokata was the lead author listed on two papers that were published in the international journal Nature. These papers (Obokata, H. et al. Nature 505, 641–647 (2014), and Obokata, H. et al. Nature 505, 676–680 (2014) described a rather simple protocol for deriving pluripotent stem cells from adult mouse cells by exposing them to acidic conditions, other types of stresses such as physical pressure on cell membranes. The cells, according to these two publications, had virtually all the characteristics of mouse embryonic stem cells, but had the added ability to form placental structures, which is an ability that embryonic stem cells do not have. The investigation initiated by the RIKEN centre comes at the behest of scientists who have noticed that some of the images used in these papers might have been duplicated from other papers. Also, several scientists have notes that they have been unable, to date, to replicate her results.

These concerns came to a head last week when the science blog PubPeer, and others, noted some problems in these two Nature papers and in an earlier paper from 2011. Obokata is also the first author of this 2011 paper (Obokata, H. et al. Tissue Eng. Part A 17, 607–15 (2011), and this paper contains a figure that seems to have been used for one of the figures in the 2014 paper. Also, there is another figure duplication.

Harvard Medical School anesthesiologist Charles Vacanti who was the corresponding author of one of the Nature papers has said that has learned last week about a data mix up in the paper and has contacted the journal to request a correction. “It certainly appears to have been an honest mistake [that] did not affect any of the data, the conclusions or any other component of the paper,” says Vacanti. Note that Vacanti is a co-author on both papers and a corresponding author on one of them.

In the other paper, Obokata serves as the corresponding author and this paper contains an image of two placentas that appear to be very similar. Teruhiko Wakayama works at Yamanashi University in Yamanashi prefecture, and he is a co-author on both of these papers. According to Wakayama, he sent more than a hundred images to Obokata and suggests that there was confusion over which to use. He says he is now looking into the problem.

Additionally, ten prominent stem-cell scientists have been unable to repeat Obokata’s results. One particular blog listed eight failures from scientists in the field. However, most of those attempts did not use the same types of cells that Obokata used.

Some scientists think that this could simply be a case of experienced scientists working with a system that they know very well and can manipulate easily, unlike outsiders to this same laboratory. For example, Qi Zhou, a cloning expert at the Institute of Zoology in Beijing, who says most of his mouse cells died after treatment with acid, says that “setting up the system is tricky; as an easy experiment in an experienced lab can be extremely difficult to others, I won’t comment on the authenticity of the work only based on the reproducibility of the technique in my lab,” says Zhou.

However, others are more deeply concerned. For example, Jacob Hanna, a stem-cell biologist at the Weizmann Institute of Science in Rehovot, Israel, however, says “we should all be cautious not to persecute novel findings” but that he is “extremely concerned and sceptical”. He plans to try for about two months before giving up.

It could be that the protocol is far more complicated that thought. For example, even Wakayama has been having trouble reproducing the results. To be sure, Wakayama and a student of his were able to replicate the experiment independently before publication, but only after being coached by Obokata. But since he moved to Yamanashi, he has had no luck. “It looks like an easy technique — just add acid — but it’s not that easy,” he says.

Wakayama says that his own success in replicating Obokata’s results has convinced him that her technique works. “I did it and found it myself,” he says. “I know the results are absolutely true.”

Clearly one way to clear this up is for the authors of this groundbreaking paper to publish a detailed protocol on how to make STAP cells. This should clear up any problems with the papers. Vacanti says he has had no problem repeating the experiment and says he will let Obokata supply the protocol “to avoid any potential for variation that could lead to confusion”.

The journal Nature has said that there are aware of the problems with the papers and looking into the matter.

For now, that’s where the issue sits. Frustrating I know, but until we know more we will have to just “wait and see.”

Histones Might Hold the Key to the Generation of Totipotent Stem Cells


Reprogramming adult cells into pluripotent stem cells remains a major challenge to stem cell research. The process remains relatively inefficient and slow and a great deal of effort has been expended to improve the speed, efficiency and safety of the reprogramming procedure.

Researchers from RIKEN in Japan have reported one piece of the reprogramming puzzle that can increase the efficiency of reprogramming. Shunsuke Ishii and his colleagues from RIKEN Tsukuba Institute in Ibaraki, Japan have identified two variant histone proteins that dramatically enhance the efficiency of induced pluripotent stem cell (iPS cell) derivation. These proteins might be the key to generating iPS cells.

Terminally-differentiated adult cells can be reprogrammed into a stem-like pluripotent state either by artificially inducing the expression of four factors called the Yamanaka factors, or as recently shown by shocking them with sublethal stress, such as low pH or pressure. However, attempts to create totipotent stem cells capable of giving rise to a fully formed organism, from differentiated cells, have failed.  However, a paper recently published in the journal Nature has shown that STAP or stimulus-triggered acquisition of pluripotency cells from mouse cells have the capacity to form placenta in culture and therefore, are totipotent.

The study by Shunsuke Ishii and his RIKEN colleagues, which was published in the journal Cell Stem Cell, attempted to identify molecules in mammalian oocytes (eggs) that induce the complete reprograming of the genome and lead to the generation of totipotent embryonic stem cells. This is exactly what happens during normal fertilization, and during cloning by means of the technique known as Somatic-Cell Nuclear Transfer (SCNT). SCNT has been used successfully to clone various species of mammals, but the technique has serious limitations and its use on human cells has been controversial for ethical reasons.

Ishii’s research group focused on two histone variants named TH2A and TH2B, which are known to be specific to the testes where they bind tightly to DNA and influence gene expression.

Histones are proteins that bind to DNA non-specifically and act as little spool around which the DNA winds.  These little wound spools of DNA then assemble into spirals that form thread-like structures.  These threads are then looped around a protein scaffold to form the basic structure of a chromosome.  This compacted form of DNA is called “chromatin,” and the DNA is compacted some 10,000 to 100,000 times.  Histones are the main arbiters of chromatin formation.  In the figure below, you can see that the “beads on a string” consist of histones with DNA wrapped around them.

DNA_to_Chromatin_Formation

There are five “standard” histone proteins: H1, H2A, H2B, H3, and H4.  H2A, H2B, H3 and H4 form the beads and the H1 histone brings the beads together to for the 30nm solenoid.  Variant histones are different histones that assemble into beads that do not wrap the DNA quite as tightly or wrap it differently than the standard histones.  Two variant histones in particular, TH2A and TH2B, tend to allow DNA wrapped into chromatin to form and more loosely packed structure that allows the expression of particular genes.

When members of Ishii’s laboratory added these two variant histone proteins, TH2A/TH2B, to the Yamanaka cocktail (Oct4, c-Myc, Sox2, and Klf4) to reprogram mouse fibroblasts, they increased the efficiency of iPSC cell generation about twenty-fold and the speed of the process two- to threefold. In fact, TH2A and TH2B function as substitutes for two of the Yamanaka factors (Sox2 and c-Myc).

Ishii and other made knockout mice that lacked the genes that encoded TH2A and TH2B. This work demonstrated that TH2A and TH2B function as a pair, and are highly expressed in oocytes and fertilized eggs. Furthermore, these two proteins are needed for the development of the embryo after fertilization, although their levels decrease as the embryo grows.

Graphical Abstract1 [更新済み]

In early embryos, TH2A and TH2B bind to DNA and induce an open chromatin structure in the paternal genome (the genome of sperm cells), which contributes to its activation after fertilization.

These results indicate that TH2A/TH2B might induce reprogramming by regulating a different set of genes than the Yamanaka factors, and that these genes are involved in the generation of totipotent cells in oocyte-based reprogramming as seen in SCNT.

“We believe that TH2A and TH2B in combination enhance reprogramming because they introduce a process that normally operates in the zygote during fertilization and SCNT, and lead to a form of reprogramming that bears more similarity to oocyte-based reprogramming and SCNT” explains Dr. Ishii.

The Speed of the Cell Cycle Makes Aging Cells Young Again


When Shinya Yamanaka and his colleagues at the RIKEN Institute discovered a way to reprogram adult cells into embryonic stem cell-like cells, known as induced pluripotent stem cells (iPSCs), they overthrew a core understanding of cell and developmental biology; namely that once cells become committed to a particular cell fate, they irreversibly remain committed to that cell fate.

Most of the work on iPSCs has examined how to increase the efficiency and safety of this reprogramming procedure. The slowness and inefficiency of this process has frustrated stem cell scientists for some time. Even though some progress has been made at increasing the efficiency of the reprogramming process, the “nuts and bolts” of why this procedure is so slow has remained unclear.

However a recent paper from the laboratory of Shangqin Guo at the Yale School of Medicine has revealed a key component of why this procedure is so slow. That component is the speed of the cell cycle or the length of time the cell takes to divide.

Fast-growing cells have lower barriers to keeping the cell committed to a particular cell fate. Thus faster-growing cells are more easily coaxed into being reprogrammed into pluripotency (the ability to differentiate into all adult cell types).

Guo’s research team examined blood cell-forming stem cells in bone marrow. Normally these stem cells are multipotent, which means that they can differentiate into a limited number of adult cell types. The particular type of blood cells that the progeny of these stem cells differentiate into depends on the particular types of growth factors available to the cells.

Guo and others found that these fast growing bone marrow stem cells could be reprogrammed in as little as four cell divisions.  Ultrafast cell cycle is a key feature of these “privileged cells” that can be reprogrammed to efficiently.  Slower-growing stem cells could not be reprogrammed nearly as fast. Thus the length of the cell cycle seemed to be the key to the speed with which cells could be reprogrammed to iPSCs.

This study also has implications for several other applications, besides making individualized iPSCs for patients. Several human diseases are associated with abnormalities in the establishment of proper cell fates and abnormalities in the cell cycle. Therefore, Guo’s paper could provide insights into why certain genetic diseases affect cells the way they do.

An Even Better Way to Make Induced Pluripotent Stem Cells


Researchers from the Centre for Genomic Regulation in Barcelona, Spain, have discovered an even faster and more efficient way to reprogram adult cells to make induced pluripotent stem cells (iPSCs).

This new discovery decreases the time it takes to derived iPSCs from adult cells from a few weeks to a few days. It also elucidated new things about the reprogramming process for iPSCs and their potential for regenerative medical applications.

iPSCs behave similarly to embryonic stem cells, but they can be created from terminally differentiated adult cells. The problem with the earlier protocols for the derivation of iPSCs is that only a very small percentage of cells were successfully reprogrammed (0.1%-2%). Also this reprogramming process takes weeks and is a rather hit-and-miss process.

The Centre for Genomic Regulation (CRG) research team have been able to reprogram adult cells very efficiently and in a very short period of time.

“Our group was using a particular transcription factor (C/EBPalpha) to reprogram one type of blood cells into another (transdifferentiation). We have now discovered that this factor also acts as a catalyst when reprogramming adult cells into iPS,” said Thomas Graf, senior group leader at the CRG and ICREA research professor.

“The work that we’ve just published presents a detailed description of the mechanism for transforming a blood cell into an iPS. We now understand the mechanics used by the cell so we can reprogram it and make it become pluripotent again in a controlled way, successfully and in a short period of time,” said Graf.

Genetic information is compacted into the nucleus like a wadded up ball of yarn. In order to access genes for gene expression, that ball of yarn has to be unwound so that the cell can find the information it needs.

The C/EBPalpha (CCAAT/Enhancer Binding Protein alpha) protein temporarily unwinds that region of DNA that contains the genes necessary for the induction of pluripotency. Thus, when the reprogramming process begin, the right genes are activated and they enable the successful reprogramming all the cells.

“We already knew that C/EBPalpha was related to cell transdifferentiation processes. We now know its role and why it serves as a catalyst in the reprogramming,” said Bruno Di Stefano, a PhD student. “Following the process described by Yamanaka the reprogramming took weeks, had a very small success rate and, in addition, accumulated mutations and errors. If we incorporate C/EBPalpha, the same process takes only a few days, has a much higher success rate and less possibility of errors, said Di Stefano.

This discovery provides a remarkable insight into stem cell-forming molecular mechanisms, and is of great interest for those studies on the early stages of life, during embryonic development. At the same time, the work provides new clues for successfully reprogramming cells in humans and advances in regenerative medicine and its medical applications.

Safe and Efficient Cell Reprogramming Inside a Living Animal


Research groups at the University of Manchester, and University College, London, UK, have developed a new technique for reprogramming adult cells into induced pluripotent stem cells that greatly reduces the risk of tumor formation.

Kostas Kostarelos, who is the principal investigator of the Nanomedicine Lab at the University of Manchester said that he and his colleagues have discovered a safe protocol for reprogramming adult cells into induced pluripotent stem cells (iPSCs). Because of their similarities to embryonic stem cells, many scientist hope that iPSCs are a viable to embryonic stem cells.

How did they do it? According to Kostarelos, “We have induced somatic cells within the liver of adult mice to transient behave as pluripotent stem cells,” said Kostarelos. “This was done by transfer for four specific gene, previously described by the Nobel-prize winning Shinya Yamanaka, without the use of viruses but simply plasmid DNA, a small circular, double-stranded piece of DNA used for manipulating gene expression in a cell.”

This technique does not use viruses, which was the technique of choice in Yamanaka’s research to get genes into cells. Viruses like the kind used by Yamanaka, can cause mutations in the cells. Kostarelos’ technique uses no viruses, and therefore, the mutagenic properties of viruses are not an issue.

Kostarelos continued, “One of the central dogmas of this emerging field is that in vivo implantation of (these stem) cells will lead to their uncontrolled differentiation and the formation of a tumor-like mass.”

However, Kostarelos and his team have determined that the technique they designed does not show this risk, unlike the virus-based methods.

“[This is the ] only experimental technique to report the in vivo reprogramming of adult somatic cells to plurpotentcy using nonviral, transient, rapid and safe methods,” said Kostarelos.

Since this approach uses circular plasmid DNA, the tumor risk is quite low, since plasmid DNA is rather short-lived under these conditions. Therefore, the risk of uncontrolled growth is rather low. While large volumes of plasmid DNA are required to reprogram these cells, the technique appears to be rather safe in laboratory animals.

Also, after a burst of expression of the reprogramming factors, the expression of these genes decreased after several days. Furthermore, the cells that were reprogrammed differentiated into the surrounding tissues (in this case, liver cells). There were no signs in any of the laboratory animals of tumors or liver dysfunction.

This is a remarkable proof-of-principle experiment that shows that reprogramming cells in a living body is fast and efficient and safe.

A great deal more work is necessary in order to show that such a technique can use useful for regenerative medicine, but it is certainly a glorious start.

 

Also involved in this paper were r, , and .

Pluripotent Stem Cells Derived From Mouse and Human White Mature Fat Cells


Several studies have shown that adult white fat cells can differentiate into other cell types by first dedifferentiating into a less committed cell type and then differentiating into heart, bone, cartilage, fat or other cell types. These dedifferentiated fat cells, which are also called DFAT cells, do not have any of the characteristics of the stem cell population normally found in fat (fat-based mesenchymal stromal cells).

No one has studied DFAT cells in much detail. One study of rat DFAT cells showed that a very low percentage of cultured rat DFAT cells (0.4% – 1.2%) expressed embryonic stem cell-specific genes after 2 weeks. Beyond that, there is little known about DFAT cells. Could they be a potential source of pluripotent cells?

A new study by Medet Jumabay and colleagues at the David Geffen School of Medicine at UCLA have isolated DFAT cells from adult white fat of mice and humans and characterized them. The results are fascinating and potentially useful for regenerative medicine.

This paper utilizes a new way to isolate fat cells that guarantees their initial purity and a culture system that encourages isolated of DFAT cells. After the fat cells were isolated from liposuction the fat cells showed the characteristics of pluripotent stem cells for five to seven days in culture. In culture, DFAT cells spontaneously clumped into clusters that expressed several stem cell-specific genes. Once these stem cell-specific genes faded, genes associated with specific cell types, such as liver or nerves, or muscle, were expressed. Interestingly, when DFAT cells were implanted into mice with non-functional immune systems, they did not form tumors.

Thus, fat-derived DFAT cells represent a highly plastic stem cell population for pluripotent cell research that is very responsive to changes in culture conditions and may benefit the development of cell-based therapies.

Stem Cell Treatments for Aortic Aneurysms


The aorta is the largest blood vessel in our bodies and it emerges from the left ventricle of the heart, takes a U-turn, and swings down toward the legs (descending or dorsal aorta). There are several branches of the aorta as it sharply turns that extend towards the head and upper extremities.

Aorta structure

Sometimes, as a result of inflammation of the aorta or other types of problems, the elastic matrix that surrounds and reinforces the aorta breaks down.  This weakens the wall of the aorta and it bulges out.  This bulge is called an aortic aneurysm and it is a dangerous condition because the aneurysm can burst, which will cause the patient to bleed to death.

Aortic Aneurysm

If an aneurysm is discovered through medical imaging techniques, drugs are given to lower blood pressure and take some of the pressure off the aorta.  Also, drugs that prevent further degradation of the elastic matrix are also used.  Ultimately, for large or fast-growing aneurysms, surgical repair of the aorta is necessary.  For aneurysms of the abdominal aorta, a surgical procedure called abdominal aortic aneurysm open repair is the “industry standard.”  For this surgery, the abdomen is cut open, and the aneurysm is repaired by the use of a long cylinder-like tube called a graft.  Such grafts are made of different materials that include Dacron (textile polyester synthetic graft) or polytetrafluoroethylene (PTFE, a nontextile synthetic graft).  The surgeon sutures the graft to the aorta, and connects one end of the aorta at the site of the aneurysm to the other end.

A “kinder, gentler” way to fix an aneurysm is to use a procedure called endovascular aneurysm repair (EVAR).  EVAR uses these devices called “stents” to support the wall of the aorta.  A small insertion is made in the groin and the collapsed stent is inserted through the large artery in the leg.  Then the stent, which is long cylinder-like tube made of a thin metal framework and covered with various materials such as Dacron or polytetrafluoroethylene (PTFE), is inserted into the aneurysm.  Once in place, the stent-graft will be expanded in a spring-like fashion to attach to the wall of the aorta and support it.  The aneurysm will eventually shrink down onto the stent-graft.

In some cases, the patient is too weak for surgery, and is not a candidate for EVAR.  A much better option would be to non-surgically repair the elastic support framework that surrounds the aorta, and stem cells are candidates for such repair.

To repair the elastic mesh work that surrounds the wall of the aorta, smooth muscle cells that secrete the protein “elastin” must be introduced into the wall of the aorta.  Also, using the patient’s own stem cells offers a better strategy at this point, since this circumvents such issues as immune rejection of implanted tissues and so on.  The sources of stem cells for smooth muscle cells include bone marrow stem cells, fat-based stem cells, and stem cells from peripheral blood.  All three of these stem cell sources have problems with finding enough cells in the body and expanding them to high enough numbers in order to properly treat the aneurysm.

Fortunately, the use of induced pluripotent stem cells, which are made from a patient’s mature cells and have many, though not all of the characteristics of embryonic stem cells, can provide large quantities of elastin-secreting smooth muscle cells.  Also, one laboratory in particular has reported differentiating human induced pluripotent stem cells into smooth muscle cells (Lee TH, Song SH, Kim KL, et al. Circ Res 106:120–128).  While there are challenges to making functional elastin, there are possibilities that many of these can be overcome.

Ideal characteristics and expected roles of iPSCs and differentiated SMC-like derivatives for treating AAAs. Shown are several of the necessary properties for expansion/differentiation in culture, delivery to the AAA, and elastogenesis within the tunica media microenvironment. Abbreviations: AAA, abdominal aortic aneurysm; ECM, extracellular matrix; Eln, elastin; iPSC, induced pluripotent stem cell; LOX, lysyl oxidase; MMPs, matrix metalloproteinases; SMC, smooth muscle cell; TNFα, tumor necrosis factor-α.
Ideal characteristics and expected roles of iPSCs and differentiated SMC-like derivatives for treating AAAs. Shown are several of the necessary properties for expansion/differentiation in culture, delivery to the AAA, and elastogenesis within the tunica media microenvironment. Abbreviations: AAA, abdominal aortic aneurysm; ECM, extracellular matrix; Eln, elastin; iPSC, induced pluripotent stem cell; LOX, lysyl oxidase; MMPs, matrix metalloproteinases; SMC, smooth muscle cell; TNFα, tumor necrosis factor-α.

In addition to induced pluripotent stem cells, other laboratories have examined umbilical cord mesenchymal stem cells and their ability to decrease the inflammation within the aorta that leads to aneurysms.  The researchers discovered that all the indicators of inflammation decreased, but the synthesis of new elastin was not examined.  However, a Japanese laboratory used mouse mesenchymal stem cells from bone marrow and found that not only did these cells shut down enzymes that tend to degrade elastin, but also initiated new elastin synthesis in culture.  The same study also showed that MSCs implanted into the vessel walls of an aorta that was experiencing an aneurysm stabilized the aneurysm by inhibiting the elastin-degrading enzymes, and increasing the elastin content of the vessel wall.  This had the net effect of stabilizing the aneurysms and preventing them from growing further (see Hashizume R, Yamawaki-Ogata A, Ueda Y, et al. J Vasc Surg 54:1743–1752).  

These experiments show that stem cell treatments for abdominal aneurysms are feasible and would definitely be a much-needed nonsurgical treatment option for the high-risk elderly demographic, which is rapidly growing in the developed world.

For more information on this interesting topic, see Chris A. BashuraRaj R. Raob and Anand Ramamurthia. Perspectives on Stem Cell-Based Elastic Matrix Regenerative Therapies for Abdominal Aortic Aneurysms.  Stem Cells Trans Med June 2013 vol. 2 no. 6 401-408.

Kidney Tubular Cells Formed from Stem Cells


A collaborative effort between several research teams has successfully directed stem cells to differentiate into kidney tubular cells. This is a significant advance that could hasten the day when stem cell-based treatments are used to treat kidney failure.

Chronic kidney disease is a major global public health problem. Unfortunately, once patients progress to kidney failure, their treatment options are limited to dialysis and kidney transplantation. Regenerative medicine, whose goal is to rebuild or repair tissues and organs, might offer a promising alternative.

A team of researchers from the Harvard Stem Cell Institute (Cambridge, Mass.), Brigham and Women’s Hospital (Boston) and Keio University School of Medicine (Tokyo) that included Albert Lam, M.D., Benjamin Freedman, Ph.D. and Ryuji Morizane, M.D., Ph.D., has been diligently developing strategies for the past five years to develop strategies to direct human pluripotent stem cells (human embryonic stem cells or hESCs and human induced pluripotent stem cells or iPSCs) to differentiate into kidney cells for the purposes of kidney regeneration.

“Our goal was to develop a simple, efficient and reproducible method of differentiating human pluripotent stem cells into cells of the intermediate mesoderm, the earliest tissue in the developing embryo that is fated to give rise to the kidneys,” said Dr. Lam. Lam also noted that these intermediate mesoderm cells would be the “starting blocks” for deriving more specific kidney cells.

Lam and his collaborators discovered a blend of chemicals which, when added to stem cells in a precise sequence, caused the stem cells to turn off their stem cell-specific genes and activate those genes found in kidney cells. Furthermore, the activation of the kidney-specific genes occurred in the same order that they turn on during embryonic kidney development.

At E10.5, the metanephric mesenchyme (red) comprises a unique subpopulation of the nephrogenic cord (yellow). Expression of the Glial-derived neurotrophic factor (Gdnf) is resticted to the metanephric mesenchyme by the actions of transcriptional activators, secreted factors, and inhibitors. GDNF binds the Ret receptor and promotes the formation of the ureteric bud, an outgrowth from the nephric duct (blue). Ret initially depends upon the Gata3 transcription factor for its expression in the nephric duct. Spry1 acts as an intracellular inhibitor of the Ret signal transduction pathway. BMP4 inhibits GDNF signaling and is in turn inhibited by the Grem1 binding protein. At 11.5, the ureteric bud has branched, forming a T-shaped structure. Each ureteric bud tip is surrounded by a cap of condensed metanephric mesenchyme. Reciprocal signaling between the cap mesenchyme and ureteric bud, as well as signals coming from stromal cells (red), maintain expression of Ret in the bud tips and Gdnf in the cap mesenchyme. Nephrons are derived from cap mesenchyme cells that form pretubular aggregates and then renal vesicles on either side of each ureteric bud tip. Wnt9b and Wnt4 induce nephron formation and are necessary for maintaining ureteric bud branching. The Six2 transcription factor prevents ectopic nephron formation. BMP7 promotes survival of the cap mesenchyme. Not all genes implicated in metanephros formation are shown for clarity (see text for further details). Green arrows indicate the ligand-receptor interaction between GDNF and Ret. Black arrows indicate the epistasis between genes but in most cases it is not known if the interactions are direct. T-shaped symbols indicate inhibitory interactions.
At E10.5, the metanephric mesenchyme (red) comprises a unique subpopulation of the nephrogenic cord (yellow). Expression of the Glial-derived neurotrophic factor (Gdnf) is resticted to the metanephric mesenchyme by the actions of transcriptional activators, secreted factors, and inhibitors. GDNF binds the Ret receptor and promotes the formation of the ureteric bud, an outgrowth from the nephric duct (blue). Ret initially depends upon the Gata3 transcription factor for its expression in the nephric duct. Spry1 acts as an intracellular inhibitor of the Ret signal transduction pathway. BMP4 inhibits GDNF signaling and is in turn inhibited by the Grem1 binding protein. At 11.5, the ureteric bud has branched, forming a T-shaped structure. Each ureteric bud tip is surrounded by a cap of condensed metanephric mesenchyme. Reciprocal signaling between the cap mesenchyme and ureteric bud, as well as signals coming from stromal cells (red), maintain expression of Ret in the bud tips and Gdnf in the cap mesenchyme. Nephrons are derived from cap mesenchyme cells that form pretubular aggregates and then renal vesicles on either side of each ureteric bud tip. Wnt9b and Wnt4 induce nephron formation and are necessary for maintaining ureteric bud branching. The Six2 transcription factor prevents ectopic nephron formation. BMP7 promotes survival of the cap mesenchyme. Not all genes implicated in metanephros formation are shown for clarity (see text for further details). Green arrows indicate the ligand-receptor interaction between GDNF and Ret. Black arrows indicate the epistasis between genes but in most cases it is not known if the interactions are direct. T-shaped symbols indicate inhibitory interactions.

The investigators were able to differentiate both hESCs and human iPSCs into cells that expressed the PAX2 and LHX1 genes, which are two key elements of the intermediate mesoderm; the developmental tissue from which the kidney develops. The iPSCs were derived by reprogramming fibroblasts obtained from adult skin biopsies into pluripotent cells. The differentiated cells expressed multiple genes found in intermediate mesoderm and spontaneously produced tubular structures that expressed those genes found in mature kidney tubules.

The researchers could then differentiate the intermediate mesoderm cells into kidney precursor cells that expressed the SIX2, SALL1 and WT1 genes. These three genes designate an embryonic tissue called the “metanephric cap mesenchyme.” Metanephric cap mesenchyme is a critical tissue for kidney differentiation. During kidney development, the metanephric cap mesenchyme contains a population of progenitor cells that give rise to nearly all of the epithelial cells of the kidney (epithelial cells or cells in a sheet, generate the lion’s share of the tubules of the kidney).

Metanephric cap mesenchyme is is red
Metanephric cap mesenchyme is is red

The cells also continued to behave like kidney cells when transplanted into adult or embryonic mouse kidneys. This gives further hope that these investigators might one day be able to create kidney tissues that could function in a patient and would be fully compatible with the patient’s immune system.

The findings are published online in Journal of the American Society of Nephrology.

Using Stem Cells for Muscle Repair


Stem cell treatments for muscular dystrophy and other degenerative diseases of muscle might be a realistic possibility, since scientists have discovered protocols to make muscle cells from human pluripotent stem cells.

Tiziano Barberi, Ph.D., chief investigator in the Australian Regenerative Medicine Institute (ARMI) at Monash University in Clayton, Victoria, and Bianca Borchin, a graduate student in the Barberi laboratory, have developed techniques to generate skeletal muscle cells. Barberi and Borchin isolated muscle precursor cells from human pluripotent stem cells (hPSCs), after which they applied a purification technique that allows these cells to differentiate further into muscle cells.

Pluripotent stem cells, such as embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs), have the ability to become any cell in the human body, including skeletal muscles, which control movement. Once the stem cells begin to differentiate, controlling that process is very challenging, but essential in order to produce only the desired cells. Barberi and Borchin used a technique known as fluorescence activated cell sorting (FACS) to identify those cells that contained the precise combination of protein markers that are expressed in muscle precursor cells. FACS also enabled them to successfully isolate those muscle precursor cells.

“There is an urgent need to find a source of muscle cells that could be used to replace the defective muscle fibers in degenerative disease. Pluripotent stem cells could be the source of these muscle cells,” Dr. Barberi said. “Beyond obtaining muscle from hPSCs, we also found a way to isolate the muscle precursor cells we generated, which is a prerequisite for their use in regenerative medicine.”

Borchin said there were existing clinical trials based on the use of specialized cells derived from hPSCs in the treatment of some degenerative diseases, but deriving muscle cells from pluripotent stem cells proved to be challenging. “These results are extremely promising because they mark a significant step towards the use of hPSCs for muscle repair,” she said.

“The production of a large number of pure muscle precursor cells does not only have potential therapeutic applications, but also provides a platform for large-scale screening of new drugs against muscle disease,” Dr. Barberi added.

This study was published early online Nov. 27 in Stem Cell Reports.  This study does not address the immune response against dystrophin that has plagued gene therapy and stem cell-based muscular dystrophy clinical trials that has been noted in previous posts.  The use of embryonic stem cells, in particular, would create muscles that are not tissue matched to the patient and would generate robust inflammation against the implanted muscles.   Thus embryonic stem cells would generate a “cure” that would be much worse than the disease itself.  Nevertheless, adapting the Barberi-Borchin protocol to induced pluripotent stem cells would produce skeletal muscle cells that are tissue matched to the patient.

Human Stem Cells Converted into Functional Lung Cells


Scientists from the Columbia University Medical Center have succeeded in transforming human stem cells into functional lung and airway cells. This finding has significant potential for modeling lung disease, screening lung-specific drugs, and, hopefully, generating lung tissue for transplantation.

Study leader, Hans-Willem Snoeck, professor of medicine and affiliated with the Columbia Center for Translational Immunology and the Columbia Stem Cell Initiative, said, “Researchers have had relative success in turning human stem cells into heart cells, pancreatic beta cells, intestinal cells, liver cells, and nerve cells, raising all sorts of possibilities for regenerative medicine. Now, we are finally able to make lung and airway cells. This is important because lung transplants have a particularly poor prognosis. Although any clinical application is still many years away, we can begin thinking about making autologous lung transplants – that is, transplants that use a patient’s own skin cells to generate functional lung tissue.”

The research builds on Snoeck’s earlier discoveries in 2011 that a set of chemical factors could induce the differentiation of embryonic or induced pluripotent stem cells into “anterior foregut endoderm,” which is the embryo in the tissue from which the lungs form (Green MD, et al. Generation of anterior foregut endoderm from human embryonic and induced pluripotent stem cells. Nat Biotechnol. 2011 Mar;29(3):267-72).

Human Embryological Development - one month

In his new study, Snoeck and his colleagues found new factors that can transform anterior foregut endoderm cells into lung and airway cells. In particular, Snoeck and his co-workers were able to establish the presence of “type 2 alveolar epithelial cells,” which secrete the lung surfactant that maintains the lung alveoli (those tiny sacs in the lung where all the oxygen exchange takes place).

lung alveolus

With these techniques, lung researchers hope to study diseases like idiopathic pulmonary fibrosis (IPF), in which type 2 epithelial cells seem to divide and produce scarring in the lungs.

“No one knows what causes the disease, and there’s no way to treat it,” said Snoeck. “Using this technology, researchers will finally be able to create laboratory models of IPF, study the disease at the molecular level, and screen drugs for possible treatments or cures. In the longer term, we hope to use this technology to make an autologous lung graft. This would entail taking a lung from a donor, removing all the lung cells, leaving only the lung scaffold; and seeding the scaffold with new lung cells derived from the patient. In this way, rejection problems could be avoided.”

Snoeck is investigating this approach in collaboration with researchers in the Columbia University Department of Biomedical Engineering.

A More Efficient Way to Grow Heart Muscle from Stem Cells Could Yield New Regenerative Therapies


An improved method to produce heart muscle from embryonic stem cells or induced pluripotent stem cells could potentially fulfill the demand for heart disease treatments and models of testing new heart drugs. The challenging part of making heart muscle in the laboratory is the production of cells that are all the same. Otherwise their response to drugs or their transplantation into a damaged heart will be unpredictable and unreliable. Fortunately a new study published in the journal STEM CELLS Translational Medicine may provide a way to make large, homogeneous batches of heart muscle cells.

By mixing some small molecules and growth factors together, an international research team led by investigators at the Cardiovascular Research Center at Icahn School of Medicine at Mount Sinai developed a two-step system that induced embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) to efficiently differentiate into ventricular heart muscle cells. This protocol was not only highly efficient but also very reproducible. It also seemed to nicely recapitulate the developmental steps of normal heart development.

“These chemically induced, ventricular-like cardiomyocytes (termed ciVCMs) exhibited the expected cardiac electrophysiological and calcium handling properties as well as the appropriate heart rate responses,” said lead investigator Ioannis Karakikes, Ph.D., of the Stanford University School Of Medicine, Cardiovascular Institute. Other members of this research team consisted of scientists from the Icahn School of Medicine at Mount Sinai, New York, and the Stem Cell & Regenerative Medicine Consortium at the University of Hong Kong.

One of the unusual aspects of this research project was the integrated approach it took. This research group combined computational and experimental systems and by using these techniques, they showed that the use of particular small molecules modulated the Wnt pathway. Signals from the Wnt pathway pass from cell to cell and play a key role in determining whether cells differentiate into an atrial or ventricular muscle cell.

“The further clarification of the molecular mechanism(s) that underlie this kind of subtype specification is essential to improving our understanding of cardiovascular development. We may be able to regulate the commitment, proliferation and differentiation of pluripotent stem cells into heart muscle cells and then harness them for therapeutic purposes,” Dr. Karakikes said.

“Most cases of heart failure are related to a deficiency of heart muscle cells in the lower chambers of the heart,” said Anthony Atala, MD, editor of STEM CELLS Translational Medicine and director of the Wake Forest Institute for Regenerative Medicine. “An efficient, cost-effective and reproducible system for generating ventricular cardiomyocytes would be a valuable resource for cell therapies as well as drug screening.”

Accelerating Stem Cells Aging To Study Age-Related Diseases Like Parkinson’s


Using stem cells to model neurodegenerative diseases shows terrific promise, but because the stem cells tend to produce young cells, they often fail to accurately model disorders that show late-onset. To solve this problem, a research group has published a paper in the December 5th edition of the journal Cell Stem Cell that describes an ingenious new method that converts induced pluripotent stem cells (iPSCs) into nerve cells that recapitulate features associated with aging as well as Parkinson’s disease. This simple approach, which involves exposing iPSC-derived cells to a protein associated with premature aging called “progerin,” could provide a way for scientists to use stem cells to model a range of late-onset disorders. This technique could potentially open new avenues for preventing and treating these devastating diseases.

“With current techniques, we would typically have to grow pluripotent stem cell-derived cells for 60 or more years in order to model a late-onset disease,” says senior study author Lorenz Studer of the Sloan-Kettering Institute for Cancer Research. “Now, with progerin-induced aging, we can accelerate this process down to a period of a few days or weeks. This should greatly simplify the study of many late-onset diseases that are of such great burden to our aging society.”

Induced pluripotent stem cells allow scientists to model a specific patient’s disease in a culture dish. By extracting a small sample of skin cells and genetically engineering them with pluripotency factors, the cells are reprogrammed into embryonic-like stem cells that have the ability to differentiate into other disease-relevant cell types like neurons or blood cells. However, iPSC-derived cells are immature and they can take months to become functional. Consequently, their slow maturation process causes iPSC-derived cells to be too young to effectively model diseases that emerge later in life.

To overcome this hurdle, Studer’s team exposed iPSC-derived skin cells and neurons that originated from both young and old donors, to a protein called “progerin.” Progerin is a mutant form of the nuclear lamin proteins that provide structure to the nuclear membrane. Mutations in these proteins cause premature aging and an early death from old age. Short-term exposure of these iPSC-derived cells to progerin caused them to manifest age-associated markers that are normally present in older cells.

Then Studer and others used iPSC technology to reprogram skin cells taken from patients with Parkinson’s disease and differentiated them into dopaminergic neurons; the type of neuron that is defective in these patients. After exposure to progerin, these cultured neurons recapitulated disease-related features, including neuronal degeneration and cell death as well as mitochondrial defects.

“We could observe novel disease-related phenotypes that could not be modeled in previous efforts of studying Parkinson’s disease in a dish,” says first author Justine Miller of the Sloan-Kettering Institute for Cancer Research. “We hope that the strategy will enable mechanistic studies that could explain why a disease is late-onset. We also think that it could enable a more relevant screening platform to develop new drugs that treat late-onset diseases and prevent degeneration.”

Understanding the Role of a Protein in Familial Alzheimer’s Disease


Lawrence Goldstein, director of the UC San Diego Stem Cell Program and a member of the Departments of Cellular and Molecular Medicine and Neurosciences, has an abiding interest in Alzheimer’s disease (AD).  To that end, he and his colleagues have used genetically engineered human induced pluripotent stem cells to determine the role a particular protein plays in the causation of familial AD.  Apparently, a simple loss-of-function model does not contribute to the inherited form of this disorder.  Goldstein hopes that his findings might be able to better explain the mechanisms behind AD and help drug makers design better drugs to treat this disease.

Familial AD is a subset of the larger group of conditions known as early-onset AD.  The vast majority of cases of AD are “sporadic” and do not have a precise known cause, even though age is a primary risk factor (an estimated 5.2 million Americans have AD).  Familial AD is causes by mutations in particular genes.  One of these genes, PS1, encodes a protein called “presenilin 1,” which acts as a protease (an enzyme that clips other proteins in half).  Presenilin 1 is the catalytic component of a protein complex called “gamma-secretase.”  Presenilin 1 forms a complex with three other proteins (Nicastrin, Aph1, Pen2) to form gamma-secretase, and this enzyme attacks specific proteins that are embedded in the cell membrane and clips them into smaller pieces.

gamma-secretase

By clipping these cell membrane proteins into smaller pieces, gamma-secretase helps the cell transport cellular material from one side of the cell membrane to the other side or form the outside of the cell to the inside.

One of the substrates of gamma-secretase is a protein called amyloid precursor protein (APP).  While the function of APP remains unknown, APP cleavage by the gamma-secretase produces small protein fragments known as amyloid beta.

A consensus among AD researchers is that the accumulation of specific forms of amyloid beta causes the formation of the amyloid plaques that kills off neurons and leads to the onset of AD.  The most abundant product of gamma-secretase cleavage of APP is a protein called “Aβ40.”  This protein is forty amino acids long and does not cause any brain damage.  However, a minority product of APP cleave by the gamma-secretase is “Aβ42,” which is 42 amino acids long and forms the amyloid plaques and neurofibillar tangles that are so characteristic of AD (see Scheuner, D., et al., Nat. Med. 2, 864–870).

According to Goldstein, most of the time, gamma-secretase clips APP without causing any problems, but some 20% of the time, the protein clips APP incorrectly and this results in the plaque-forming forms of amyloid beta.  Goldstein explained: “Our research demonstrates very precisely that mutations in PS1 double the frequency of bad cuts.”

To demonstrate this, Goldstein and his co-workers purchased human induced pluripotent stem cells and differentiated them into neurons.  These neurons contained different alleles (forms) of the PS1 gene, and some of these mutant forms of PS1 contained the types of mutations that cause familial AD.  Once PS1 allele in particular called PS1 ΔE9 increased the ratio of Aβ42 to Aβ40 dose-dependent manner.  Since the PS1 ΔE9 causes familial AD, this research elucidates precisely why it does so.

“We were able to investigate exactly how specific mutations and their frequency change the behavior of neurons.  We took finely engineered cells that we knew and understood and then looked how a single mutation causes changed in the molecular scissors and what happened next.”

Presenilin allele consequences

Goldstein further notes, “In some ways, this is a powerful technical demonstration of the promise of stem cells and genomics research in better understanding and ultimately treating AD.  We were able to identify and assign precise limits on how a mutations works in familial AD.  That’s an important step in advancing the science, in finding drugs and treatments that can slow, maybe reverse, the disease’s devastating effects.”

Physical Cues Push Mature Cells into Induced Pluripotent Stem Cells


Bioengineers from the laboratory of Song Li at UC Berkeley have used physical cues to help push mature cells to de-differentiate into embryonic-like cells known as induced pluripotent stem cells.

Essentially, Li and his coworkers grew skin fibroblasts from human skin and mouse ears on surfaces with parallel grooves 10 micrometers apart and 3 micrometers high, in a special culture medium. This procedure increased the efficiency of reprogramming of these mature cells four-fold when compared to cells grown on a flat surface. Growing cells in scaffolds of nanofilbers aligned in parallel had similar effects.

Li’s study could significantly advance the protocols for making induced pluripotent stem cells (iPSCs). Normally iPSCs are made by genetically engineering adult cells so that they overexpress four different genes: Oct-4, Sox-2, Klf-4, and c-Myc. To put these genes into the cells, genetically modified viruses are used, or plasmids (small circles of DNA). Initially, Shinya Yamanaka, the scientist who invented iPSCs, and his co-workers used retroviruses that contained these four genes. When fibroblasts were infected with these souped-up retroviruses, the viruses inserted their viral DNA into the genomes of the host cells and expressed these genes.

retrovirus_life_cycle

Shinya Yamanaka won the Nobel Prize for this work in Physiology or Medicine in 2012 for this work. Unfortunately, retroviruses and can cause insertional mutations when they integrate into the genome (Zheng W., et al., Gene. 2013 Apr 25;519(1):142-9), and for this reason they are not the preferred way of making iPSCs. There are other viral vectors that do not integrate into the genome of the host cell (e.g., Sendai virus; see Chen IP, et al., Cell Reprogram. 2013 Dec;15(6):503-13). There are also techniques that use plasmids, which encode the four genes but do not integrate into the genome of the host cell. Finally, synthetic messenger RNAs that encode these four genes have also been used to make iPSCs (Tavernier G,, et al., Biomaterials. 2012 Jan;33(2):412-7).

The use of physical cues to make iPSCs may replace the need for gene overexpression, just as the use of particular chemicals can replace the need for particular genes (Zhu, S. et al. Cell Stem Cell 7, 651–655 (2010); Li, Y. et al. Cell Res. 21, 196–204 (2011)). If physical cues can replace the need for the overexpression of particular genes, then this discovery could revolutionize iPSC derivation; especially since the overexpression of particular genes in mature cells tends to cause genome instability in cells (Doris Steinemann, Gudrun Göhring, and Brigitte Schlegelberger. Am J Stem Cells. 2013; 2(1): 39–51).

“Our study demonstrates for the first time that the physical features of biomaterials can replace some of these biochemical factors and regulate the memory of a cell’s identity,” said study principal investigator Song Li, UC Berkeley, Professor of bioengineering. “We show that biophysical signals can be converted into intracellular chemical signals that coax cells to change.”

a, Scanning electron micrograph of PDMS membranes with a 10 μm groove width. All grooves were fabricated with a groove height of 3 μm. b, The top row shows phase contrast images of flat and grooved PDMS membranes with various widths and spacings. The bottom row shows fibroblast morphology on various PDMS membranes. Images are fluorescence micrographs of the nucleus (DAPI, blue) and actin network (phalloidin, green; scale bars, 100 μm). c, Reprogramming protocol. Colonies were subcultured and expanded or immunostained and quantified by day 12–14. d, Fluorescence micrograph showing the morphology of iPSC colonies generated on flat and grooved membranes (scale bar, 1 mm). Groove dimensions were 10 μm in width and spacing, denoted as 10 μm in this and the rest of the figures. Double-headed arrow indicates microgroove orientation of alignment. e, Reprogramming efficiency of fibroblasts transduced with OSKM and cultured on PDMS membranes with flat or grooved microtopography. The number of biological replicates, n, used for this experiment was equal to 6. Groove width and spacing were varied between 40, 20 and 10 μm. Differences of statistical significance were determined by a one-way ANOVA, followed by Tukey’s post-hoc test. * indicates significant difference (p<0.05) compared with the control flat surface. f, Reprogramming efficiency in fibroblasts transduced with OSK (n = 4). *p<0.05 (two-tailed, unpaired t-test) compared with the control flat surface. Error bars represent one standard deviation. g, Immunostaining of a stable iPSC line expanded from colonies generated on 10 μm grooves. These cells express mESC-specific markers Oct4, Sox2, Nanog and SSEA-1 (scale bar, 100 μm). h, The expanded iPSCs in g were transplanted into SCID mice to demonstrate the formation of teratomas in vivo (scale bar, 50 μm).
a, Scanning electron micrograph of PDMS membranes with a 10 μm groove width. All grooves were fabricated with a groove height of 3 μm. b, The top row shows phase contrast images of flat and grooved PDMS membranes with various widths and spacings. The bottom row shows fibroblast morphology on various PDMS membranes. Images are fluorescence micrographs of the nucleus (DAPI, blue) and actin network (phalloidin, green; scale bars, 100 μm). c, Reprogramming protocol. Colonies were subcultured and expanded or immunostained and quantified by day 12–14. d, Fluorescence micrograph showing the morphology of iPSC colonies generated on flat and grooved membranes (scale bar, 1 mm). Groove dimensions were 10 μm in width and spacing, denoted as 10 μm in this and the rest of the figures. Double-headed arrow indicates microgroove orientation of alignment. e, Reprogramming efficiency of fibroblasts transduced with OSKM and cultured on PDMS membranes with flat or grooved microtopography. The number of biological replicates, n, used for this experiment was equal to 6. Groove width and spacing were varied between 40, 20 and 10 μm. Differences of statistical significance were determined by a one-way ANOVA, followed by Tukey’s post-hoc test. * indicates significant difference (p<0.05) compared with the control flat surface. f, Reprogramming efficiency in fibroblasts transduced with OSK (n = 4). *p

To boost the efficiency of mature cell reprogramming, scientists also use a chemical called valproic acid, which dramatically affects global DNA structure and expression.

“The concern with current methods is the low efficiency at which cells actually reprogram and the unpredictable long-term effects of certain imposed genetic or chemical manipulations,” said the lead author of this study Timothy Downing. “For instance, valproic acid is a potent chemical that drastically alters the cell’s epigenetic state and can cause unintended changes inside the cell. Given this, many people have been looking at different ways to improve various aspects of the reprogramming process.”

This new study confirms and extends previous studies that showed that mechanical and physical cues can influence cell fate. Li’s group showed that physical and mechanical cues can not only affect cell fate, but also the epigenetic state and cell reprogramming.

a, Scanning electron micrograph of nanofibres showing fibre morphology in aligned and random orientations (scale bar, 20 μm). Confocal fluorescence micrograph of fibroblasts cultured on nanofibres (DAPI (blue) and phalloidin (green) staining; scale bar, 100 μm). b, Western blotting analysis for fibroblasts cultured on random and aligned nanofibres for three days. c, Fibroblasts were transduced with OSKM and seeded onto nanofibre surfaces, followed by immunostaining for Nanog expression (red) at day 12. Nuclei were stained with DAPI in blue; scale bar, 500 μm. d, Quantification of colony numbers in c (n = 5). *p<0.05 (two-tailed, unpaired t-test) compared with the control surface with random nanofibres. e, Fibroblasts were micropatterned into single-cell islands of 2,000 μm2 area with a CSI value of 1 (round) or 0.1 (elongated). After 24 h, cells were immunostained for AcH3, H3K4me2 or H3K4me3 (in green). Phalloidin staining (red) identifies the cell cytoskeleton for cell shape accuracy. The white arrowhead indicates the location of the nucleus (scale bars, 20 μm). f, Quantification of fluorescence intensity in e (n = 34, 20 and 34 for AcH3, H3K4me2 and H3K4me3, respectively). *p<0.05 (two-tailed, unpaired t-test) compared with the circular micropatterned cells (CSI = 1). Error bars represent one standard deviation.
a, Scanning electron micrograph of nanofibres showing fibre morphology in aligned and random orientations (scale bar, 20 μm). Confocal fluorescence micrograph of fibroblasts cultured on nanofibres (DAPI (blue) and phalloidin (green) staining; scale bar, 100 μm). b, Western blotting analysis for fibroblasts cultured on random and aligned nanofibres for three days. c, Fibroblasts were transduced with OSKM and seeded onto nanofibre surfaces, followed by immunostaining for Nanog expression (red) at day 12. Nuclei were stained with DAPI in blue; scale bar, 500 μm. d, Quantification of colony numbers in c (n = 5). *p

“Cells elongate, or example, as they migrate throughout the body,” said Downing, who is a research associate in Li’s lab. “In the case of topography, where we control the elongation of a cell by controlling the physical microenvironment, we are able to more closely mimic what a cell would experience in its native physiological environment. In this regard, these physical cues are less invasive and artificial to the cell and therefore less likely to cause unintended side effects.”

Li and his colleagues are studying whether growing cells on grooved surfaces eventually replace valproic acid and even replace other chemical compounds in the reprogramming process.

“We are also studying whether biophysical factors could help reprogram cells into specific cell types, such as neurons,” said Jennifer Soto, a UC Berkeley graduate student in bioengineering who was also a co-author on this paper.

Timothy Downing, et al., Nature Materials 12, 1154–1162 (2013).  

Stem-Based Treatment of Stoke


When blood flow to the brain ceases as the result of a blood clot, trauma, or injury, the brain suffers from a shortage of oxygen. Such an incident is known as a stroke and it can result in the death of neurons and the loss of those functions to which the dead neurons contributed. Treatment for stroke is largely supportive, but regenerative treatments that replace the dead neurons would be the most ideal treatment.

A research consortium at Lund University in Lund, Sweden has found that neurons made from induced pluripotent stem cells integrate into the brains of mice that had suffered strokes. This experiment takes a closer step towards the development of a regenerative treatment for strokes.

Strategies for stem cell-based regenerative therapy in neurodegenerative diseases.
Strategies for stem cell-based regenerative therapy in neurodegenerative diseases.

In the aftermath of a stroke, nerve cells in the brain die. At the Lund Stem Cell Center, the research groups of Zaal Kokaia and Olle Lindvall teamed up to develop a stem cell-based method to treat stroke patients.

After a stroke, the cerebal cortex tends to take the bulk of the damage and neuron loss from the cerebral cortex underlies many of the symptoms following a stroke, such a paralysis and speech problems. The method developed by the Lund Institute scientists should make it possible to generate nerve cells for transplantation from the patient’s own skin cells.

Transient-Ischemic-Attack

First, the Lund team isolated skin fibroblasts from the afflicted mice and used genetic engineering techniques to convert them into induced pluripotent stem cells (iPSCs), which have many of the differentiation capabilities of embryonic stem cells. These iPSC lines were differentiated into cortical neurons, which tend to populate the cerebral cortex. However, transplanting fully differentiated neurons into the brain tend to not work terribly well because the mature neurons are unable to divide and have poor abilities to connect with other cells. Therefore, the neuron progenitor cells that will give rise to cortical neurons are a better candidate for transplantation.

After generating long-term self-renewing neuroepithelial-like stem cells from iPSCs in the laboratory, the Lund group scientists showed that these stem cells could give rise to neural progenitors that expressed the types of genes found in mature cortical neurons. When these neural progenitor cells were transplanted into rats that had suffered strokes, two months after transplantation, the cortically fated cells showed less proliferation and more efficient differentiation into mature neurons with the right shape, size, and structure of cortical neurons and expressed the same proteins as cortical neurons. These tranplanted cells also extended more axons than those cells that were not fated to form cortical neurons. Transplantation of both the cortical neuron-fated and non-cortical neuron-fated cells caused recovery of the impaired function in the stepping test in comparison to controls. At 5 months after stroke, there was no tumor formation and the grafted cells had all the electrophysiological properties of mature neurons and showed full evidence that they had integrated into the existing neural circuitry.

These results are very promising and represent a very early but important step towards a stem cell-based treatment for stroke in patients. Further experimental studies are necessary if these experiments are to be translated into the clinic in a responsible way.

Foregut Stem Cells


Scientists from Cambridge University have designed a new protocol that will convert pluripotent stem cells into primitive gut stem cells that have the capacity to differentiate into liver, pancreas, or some other gastrointestinal structure.

Nicholas Hannan and his colleagues at the University of Cambridge Welcome Trust MRC Stem Cell Institute have developed a technique that allows researchers to grow a pure, self-renewing population of stem cells that are specific to the human foregut, which is the upper section of the human digestive system. These types of stem cells are known as “foregut stem cells” and they can be used to make liver, pancreas, stomach, esophagus, or even parts of the small intestine. Making these types of gastrointestinal tissues can provide material for research into gastrointestinal abnormalities, but might also serve as a source of material to treat type 1 diabetes, liver disease, esophageal and stomach cancer, and other types of severe gastrointestinal diseases.

“We have developed a cell culture system which allows us to specifically isolate foregut stem cells in the lab,” said Hannan. “These cells have huge implications for regenerative medicine, because they are the precursors to the thyroid upper airways, lungs, liver, pancreas, stomach, and biliary systems.”

Hannan did this work in the laboratory of Ludovic Vallier, and they think that their technique will provide the means to analyze the precise embryonic development of the foregut in greater detail. “We now have a platform from which we can study the early patterning events that occur during human development to produce intestines, liver, lungs, and pancreas,” said Hannan.

To make foregut stem cells, Hannan begins with a pluripotent stem cell line; either an embryonic stem cell line or an induced pluripotent stem cell line. Then he differentiated them into definitive endoderm by treating them with CDM-PVA and activin-A (100 ng/ml), BMP4 (10 ng/ml), bFGF (20 ng/ml), and LY294002 (10 mM) for 3 days. Once they differentiated into endoderm, the endodermal cells were grown in RPMI+B27 medium with activin-A (50 ng/ml) for 3-4 days in order to generate foregut stem cells.

(A) GFP-expressing hPSCs were differentiated into hFSCs. (B) Single GFP-positive hFSCs were seeded onto a layer of non-GFP hFSCs and then expanded for five passages. The resulting population was then split into culture conditions inductive for liver or pancreatic differentiation. (C and D) GFP-hFSCs differentiated for 25 days were found to respectively generate cells expressing liver markers (ALB, LDL-uptake) and pancreatic markers (PDX1, C-peptide) from both hESC-derived (C) and hIPSC-derived (D) hFSCs.
(A) GFP-expressing hPSCs were differentiated into hFSCs.  (B) Single GFP-positive hFSCs were seeded onto a layer of non-GFP hFSCs and then expanded for five passages. The resulting population was then split into culture conditions inductive for liver or pancreatic differentiation.  (C and D) GFP-hFSCs differentiated for 25 days were found to respectively generate cells expressing liver markers (ALB, LDL-uptake) and pancreatic markers (PDX1, C-peptide) from both hESC-derived (C) and hIPSC-derived (D) hFSCs.

These foregut stem cells (FSCs) can self-renew, and can also differentiate into any part of the foregut. Thus, FSCs can grow robustly in culture, and they can also differentiate into foregut derivatives. However, these cells also do not form tumors. When injected into mice, they failed to form tumors.

(A) Large cystic hFSC outgrowth under the kidney capsule of a NOD-SCID mouse. (B) Cryosection of a hFSC outgrowth showing large cystic structures lined with epithelial cells. (C) Immunocytochemistry showing foregut outgrowths expressing EpCAM, PDX1, AFP, and NKX2.1. Scale bars, 100 μm or 50 μm as shown. See also Figure S4.
(A) Large cystic hFSC outgrowth under the kidney capsule of a NOD-SCID mouse.  (B) Cryosection of a hFSC outgrowth showing large cystic structures lined with epithelial cells.  (C) Immunocytochemistry showing foregut outgrowths expressing EpCAM, PDX1, AFP, and NKX2.1.  Scale bars, 100 μm or 50 μm as shown. See also Figure S4.

What are the advantages to FSCs as opposed to making pancreatic cells or liver cells from pluripotent stem cells? These types of experiments always create cultures that are impure. Such cultures are difficult to use because not all the cells have the same growth requirements and they would be dangerous for therapeutic purposes because they might contain undifferentiated cells that might grow uncontrollably and cause a tumor. Therefore, FSCs provide a better starting point to make pure cultures of pancreatic tissues, liver tissues, stomach tissues and so on.

Ludovic Vallier, the senior author of this paper said this of his FSCs, “What we have now is a better starting point – a sustainable platform for producing liver and pancreatic cells. It will improve the quality of the cells that we produce and it will allow us to produce the large number of uncontaminated cells we need for the clinical applications of stem cell therapy.”

Vallier’s groups is presently examining the mechanisms that govern the differentiation of FSCs into specific gastrointestinal cell types in order to improve the production of these cells for regenerative medicine.

Induced Pluripotent Stem Cells Do Not Cause Immune Rejection


A paper appeared in the journal PLoS One by Liu and others that showed that heart muscle cells made from induced pluripotent stem cells were rejected by the immune system of mice. The way induced pluripotent stem cells (iPSCs) are made introduces mutations, many of which are harmless. However, mutations that alter the cell surface proteins of iPSC derivatives can cause the immune system of the host to attack and destroy any transplanted cells.

Are adult cells made from iPSC recognized by the immune system? Are the mouse experiments merely an anomaly of the mouse system?

Dr. Jun Takahashi of Kyoto University’s Center for iPS Cell Research and Application and his research group have examined how monkeys respond to implanted derivatives of iPSCs. They made iPSCs from monkey cells taken from the inside of the mouth. Then Takahashi and his group made midbrain-specific neurons from them and transplanted them back into the monkeys. Only a minimal immune response against these cells was observed. However if a monkey received midbrain neurons made from another animal’s cells, then a robust immune response followed.

Therefore, in non-human primates, iPSC derivatives are not rejected by the immune system of the host.

Takahashi said of this experiment, “These findings give a rationale to start autologous transplantation – at least of neural cells – in clinical situations.”  Takahashi’s last statement is critically important – “At least of neural cells.” The brain is an immunologically privileged organ that normally does not have immune cells lurking in its midst. The heart, however, is constantly under immunological surveillance. Therefore, even though this experiment shows that IPSC derivatives are not rejected in non-human primates under these circumstances, there might be circumstances under which they are rejected.

Since there are ways to screen iPSCs and their derivatives for mutations that might sensitize the immune system to the host, such screenings could almost certainly decrease the rate of immunological rejection. Such screening were not done in either this experiment or in the experiments of Liu and others.

Cardiac Muscle Repair with Molecular Beacons


Pure heart muscle cells that are ready for transplantation. This is one of the Holy Grails of regenerative medicine. Of course when working with pluripotent stem cell lines, isolating nothing but beating heart muscle cells is rather difficult. A new technique makes the isolation of pure cultures of beating heart muscle cells that much easier.

Researchers at Emory and Georgia Tech have developed a method that utilizes molecules called “molecular beacons” to isolate heart muscle cells from pluripotent stem cells. Molecular beacons fluoresce when they come into contact with cells that express certain genes. In this case, the beacons target cells that express heart-specific myosin.

Physicians can use these purified cardiac muscle cells to heal damaged areas of the heart in patient that have suffered a heart attack or are suffering heart failure. This molecular beacon technique might also have applications in other fields of regenerative medicine as well.

“Often, we want to generate a particular cell population from stem cells for introduction into patients,” said Young-sup Yoon, professor of medicine and director for stem cell biology at Emory University School of Medicine. “But the desired cells often lack a readily accessible surface marker, or that marker is not specific enough, as is the case for cardiac muscle cells. This technique could allow us to purify almost any type of cell.”

Gang Bao pioneered he use of molecular beacons and was a co-author of this publication. Yoon and is colleagues and collaborators grew mouse and human embryonic stem cells and induced pluripotent stem cells and differentiated them into heart muscle cells (cardiomyocytes). They then used molecular beacons to label only those cells that expressed messenger RNAs with just the right sequences. These molecular beacons hybridized with the mRNAs and fluoresced. Bao and others then used flow cytometry to sort the fluorescent cells from the non- fluorescent cells. The fluorescent cells have differentiated into heart muscle cells and were isolated from all the other cells.

These purified heart muscle cells could engraft into the heart of a mouse that had suffered a heart attack and they improved heart function and formed no tumors. This proof-of-principle experiment shows that this technique is feasible.

“In previous experiments with injected bare cells, investigators at Emory and elsewhere found that a large proportion of the cells are washed away. We need to engineer the cells into compatible biomaterials to enhance engraftment and retention,” said Yoon,

Do Stem Cells from Bone Outdo Those from the Heart in Regenerating Cardiac Tissue?


Scientists at Tulane University in New Orleans, La. (US) have completed a study that suggests that stem cells derived from cortical, or compact bone do a better job of regenerating heart tissue than do the heart’s own stem cells.

The study, led by Steven R. Houser, Ph.D., FAHA, director of Tulane’s School of Medicine’s Cardiovascular Research Center (CVRC), could potentially lead to an “off the rack” source of stem cells for regenerating cardiac tissue following a heart attack.

Cortical bone stem cells (CBSCs) are considered some of the most pluripotent cells in the adult body. These cells are naïve and ready to differentiate into just about any cell type. However, even though CBSCs and similar pluripotent stem cells retain the ability to develop into any cell type required by the body, they have the potential to wander off course and land in unintended tissues. Cardiac stem cells, on the other hand, are more likely to stay in their resident tissue.

Bone cross-section

To determine how CBSCs might behave in the heart, Houser’s team, led by Temple graduate student Jason Duran, collected the cells from mouse tibias (shin bones), expanded them in the lab and then injected them into back the mice after they had undergone a heart attack.

The cells triggered the growth of new blood vessels in the injured tissue and six weeks after injection had differentiated into heart muscle cells. While generally smaller than native heart cells, the new cells had the same functional capabilities and overall improved survival and heart function.

Similar improvements were not observed in mice treated with cardiac stem cells, nor did those cells show evidence of differentiation.

“What we did generates as many questions as it does answers,” Dr. Houser said. “Cell therapy attempts to repopulate the heart with new heart cells. But which cells should be used, and when they should be put into the heart are among many unanswered questions.”

The next step will be to test the cells in larger animal models. The current study was published in the Aug. 16 issue of Circulation Research.