New Type of Stem Cell Discovered by Salk Scientists


Stem cell scientists from the laboratory of Juan Carlos Izpisua Belmonte at the Salk Institute for Biological Studies in La Jolla, California have discovered a new type of stem cell that could potentially provide a model system for early human development, and might even allow human organs to be grown in large animals for therapeutic purposes.

 

Izpisua Belmonte and his colleagues came across these types of cells somewhat serendipitously while transplanting human pluripotent stem cells into mouse embryos.

 

Other types of pluripotent stem cells have already been well-known to stem cell scientists for some time. Stem cells are “pluripotent,” if they have an intrinsic ability to differentiate into any adult cell type. Embryonic stem cells (ESCs), for example, are derived from early human embryos that have yet to implant into the inner layer of the uterus.  However, epiblast stem cells (EpiSCs) have been established from post-implantation embryos and have different properties.  While both are pluripotent, they bear striking differences in molecular signature, signalling dependency, colony morphology, cloning efficiency, metabolic requirements and epigenetic features (see Nichols, J. & Smith, A. Cell Stem Cell 4, 487492 (2009) and Zhou, W. et al. EMBO J. 31, 21032116 (2012)).  Both of these cells have the ability to re-enter embryogenesis but they do so at different developmental time points (pre-implantation versus post-implantation, respectively), which distinguish ESCs and EpiSCs.  Therefore, these two cell types exist in two temporally distinct pluripotent states.  Even though these two types of pluripotent stem cells can be grown into large numbers in the laboratory, differentiating them into specific types of mature, adult cells has proven difficult in some cases. The cells discovered by Izpisua Belmonte and his colleagues are reportedly easier to grow in vitro and engraft into an embryo if they are injected into the right spot. Izpisua Belmonte call these cells “region-selective pluripotent stem cells” (rsPSCs).

 

 

Because rsPSCs grow more quickly and stably than other pluripotent cells, they may be more useful for developing new therapies, according to Paul Tesar, a developmental biologist at Case Western Reserve University in Cleveland, Ohio.

 

Izpisua Belmonte and colleagues originally wanted to transplant various types of human pluripotent stem cells into mouse embryos in the laboratory. They prepared their cells for transplantation by growing them in various blends of culture media that contained different combinations of growth factors and other chemicals. They found that one particular blend was more effective at making the cells grow and proliferate. However, the cells that grew quite well in this concoction displayed different patterns of metabolism and gene expression in comparison to other pluripotent stem cells. These same cells not graft well into the mouse embryo.

 

Thus, Izpisua Belmonte and his colleagues decided to nail down those features that would cause cells to efficiently integrate into mouse embryos. They injected the human cells into three different regions of a 7.5-day-old mouse embryo. Thirty-six hours later, only those cells that had been grafted into the tail, or posterior of the embryo, integrated and differentiated into the correct cell layers to form a “chimeric” or mixed-tissue embryo. Such organisms contain cells with genomes from DNA organisms. Since these cells seemed to prefer one part of the embryo, Izpisua Belmonte and his team called them region-selective pluripotent stem cells.

 

From these data, Izpisua Belmonte has proposed that embryos contain multiple types of pluripotent stem cells, including rsPSCs, during their early development. It is not yet clear whether the rsPSCs play a part in designating which part of the embryo will become the head, the middle, or hind end. Identifying various types of pluripotent cells might provide researchers with the ability to study the early stages of human embryonic development by transplanting rsPSCs into animal embryos.

 

Izpisua Belmonte and his colleagues found that they could easily use enzymes that modify the sequences of DNA to edit the genomes of rsPSCs, which is usually difficult to do in pluripotent cell lines when grown in culture.

Gene editing could help scientists to optimize the ability of human cells to grow within animals, which might allow the creation of transgenic chimeras. Tesar says that the idea of using human pluripotent cells, such as rsPSCs, to create animals with human organs is not unrealistic, but he expects that it will be very difficult. The immune system of the animal might reject the human cells and the growth rates of the two organs might also cause problems.

Izpisua Belmonte’s lab is already starting to implant pig embryos with a different type of stem cells, and this is the only very first step for these techniques.

 

A New Way to Mend Broken Hearts


Salk Institute researchers have discovered a way to heal injured hearts by reactivating long dormant molecular machinery found in the heart cells. This significant finding could open the door to new therapies for heart disorders in humans.

These new results were published in the November 6th, 2014 edition of the journal Cell Stem Cell. Although adult mammals don’t normally regenerate damaged tissue, they seem to retain a latent ability to do so. When the Salk team inhibited four different molecules that suppress genetic programs that lead to organ regeneration, they observed a dramatic improvement in heart regeneration and healing in laboratory mice.

These experiments provide proof-of-concept for a new type of clinical treatment in the fight against heart disease, which, according to the US Centers for Disease Control and Prevention, kills about 600,000 people each year in the United States alone.

“Organ regeneration is a fascinating phenomenon that seemingly recapitulates the processes observed during development. However, despite our current understanding of how embryogenesis and development proceeds, the mechanisms preventing regeneration in adult mammals have remained elusive,” says the study’s senior author Juan Carlos Izpisua Belmonte, holder of the Roger Guillemin Chair and primary investigator in the Gene Expression Laboratory and the Salk Institute.

We have within every cell of our bodies, the genes for organ regeneration. For several years, Izpisua Belmonte and his coworkers have attempted to clarify the genes that organism uses during embryonic development and during tissue healing highly regenerative organisms such as the zebrafish.

An injured zebrafish heart showing proliferating cells in the wounded area of the heart (red) and cardiac muscle cells (green).
An injured zebrafish heart showing proliferating cells in the wounded area of the heart (red) and cardiac muscle cells (green).

In 2003, Izpisua Belmonte’s laboratory first identified the signals that precede zebrafish heart regeneration, which they followed-up with a 2010 Nature paper, in which scientists from Izpisua Belmonte’s laboratory described how regeneration occurred in the zebrafish. Rather than stem cells invading injured heart tissue, the cardiac cells themselves reverted to a precursor-like state (a process called ‘dedifferentiation’). Dedifferentiation allowed the cells to proliferate within the damaged tissue.

n a dish, heart muscle cells return to a precursor-like state after pro-regenerative treatment with microRNA inhibitors. Green shows a disorganized cardiomyocyte cytoskeleton indicative of cell dedifferentiation; red shows mitochondrial organization.
In a dish, heart muscle cells return to a precursor-like state after pro-regenerative treatment with microRNA inhibitors. Green shows a disorganized cardiomyocyte cytoskeleton indicative of cell dedifferentiation; red shows mitochondrial organization.

They next determined if mammals retained any of the molecular players responsible for this kind of regenerative reprogramming. However, such an experiment came with some risks, recalls Ignacio Sancho-Martinez, a postdoctoral researcher in Izpisua Belmonte’s lab.

“When you speak about these things, the first thing that comes to peoples’ minds is that you’re crazy,” he says. “It’s a strange-sounding idea, since we associate regeneration with salamanders and fish, but not mammals.”

What are the things that cause a heart to regenerate in these smaller animals? Extensive work on the regenerating hearts of fish and salamanders failed to reveal anything concrete. Therefore, the laboratory changed its tack. “Instead, we thought, ‘If fish know how to do it, there must be something they can teach us about it,’” says the study’s first author Aitor Aguirre, a postdoctoral researcher in Izpisua Belmonte’s group.

The team focused on microRNAs, which control the expression of many genes. They used an extensive genetic screen for microRNAs that changed their expression levels during the healing of the zebrafish heart and that were found in the mammalian genome.

Their studies uncovered four molecules in particular–MiR-99, MiR-100, Let-7a and Let-7c–that fit their criteria. All were heavily repressed during heart injury in zebrafish and they were also present in rats, mice and humans.

However, in studies of mammalian cells in a culture dish and studies of living mice with heart damage, the group saw that the levels of these molecules were high in adults and failed to decline after the heart experienced injury. Therefore, Izpisua Belmonte’s team used adeno-associated viruses that could specifically infect the heart to target each of those four microRNAs and experimentally suppress their expressing levels.

Injecting these inhibitors into the hearts of mice that had suffered a heart attack triggered the regeneration of cardiac cells, and improved numerous physical and functional aspects of the heart, such as the thickness of its walls and its ability to pump blood. The scarring caused by the heart attack was significantly reduced with treatment compared to controls.

The improvements were still obvious three and six months after treatment–a long time in a mouse’s life. “The good thing is that the success was not limited to the short-term, which is quite common in cardiac regenerative biology,” Sancho-Martinez says.

The new study focused only on a handful of 70 some microRNA candidates that turned up in their initial screen. These other molecules might also play a part in heart cell proliferation, healing scars and promoting the formation of new blood vessels–all processes critical for heart repair, Sancho-Martinez says. The data are available so that other research groups can focus on molecules that interest them.

The next step for Izpisua Belmonte’s team is to move into larger animals and see whether “regenerative reprogramming” can work in larger hearts, and for extended periods after treatment, says Sancho-Martinez. And, although the virus packaging disappeared from the animals’ bodies by 2 weeks after treatment, the scientists are working on a new way to deliver the inhibitors to avoid the need for viruses altogether.

Directly Reprogramming Skin Cells into White Blood Cells


Scientists from the Salk Institute have, for the first time, directly converted human skin cells into transplantable white blood cells, which are the soldiers of the immune system that fight infections and invaders. This work could prompt the creation of new therapies that introduce new white blood cells into the body that can attack diseased or cancerous cells or augment immune responses for other conditions.

This work, which shows that only a small amount of genetic manipulation could prompt this direct conversion, was published in the journal Stem Cells.

“The process is quick and safe in mice,” says senior author Juan Carlos Izpisua Belmonte, who holds the Salk’s Roger Guillemin Chair. “It circumvents long-standing obstacles that have plagued the reprogramming of human cells for therapeutic and regenerative purposes.”

The problems that Izpisua Belmonte mentions, includes the long time (at least two months) numbingly tedious cell culture work it takes to produce, characterize and differentiate induced pluripotent stem (iPS) cells. Blood cells derived from iPSCs also have other obstacles: they engraft into organs or bone marrow poorly and can cause tumors.

The new method designed by Izpisua Belmonte and his team, however, only takes two weeks, does not produce tumors, and engrafts well.

“We tell skin cells to forget what they are and become what we tell them to be—in this case, white blood cells,” says one of the first authors and Salk researcher Ignacio Sancho-Martinez. “Only two biological molecules are needed to induce such cellular memory loss and to direct a new cell fate.”

This faster reprogramming technique developed by Belmonte’s team utilized a form of reprogramming that does not go through a pluripotency stage. Such techniques are called indirect lineage conversion or direct reprogramming. Belmonte’s group has demonstrated that such approaches can reprogram cells to form the cells that line blood vessels. Thus instead of de-differentiating cells into an embryonic stem cell-type stage, these cells are rewound just enough to instruct them to form the more than 200 cell types that constitute the human body.

Direct reprogramming used in this study uses a molecule called SOX2 to move the cells into a more plastic state. Then, the cells are transfected with a genetic factor called miRNA125b that drives the cells to become white blood cells. Belmonte and his group are presently conducting toxicology studies and cell transplantation proof-of-concept studies in advance of potential preclinical and clinical studies.

“It is fair to say that the promise of stem cell transplantation is now closer to realization,” Sancho-Martinez says.

Study co-authors include investigators from the Center of Regenerative Medicine in Barcelona, Spain, and the Centro de Investigacion Biomedica en Red de Enfermedades Raras in Madrid, Spain.

Scientists Generate “Mini-kidney” Structures from Human Stem Cells


Kidney Disease represents a major and unsolved health issue worldwide. Once damaged by disease, kidneys rarely recover their original level of function, and this highlights the urgent need for better knowledge of kidney development and physiology.

Now, a team of researchers led by scientists at the Salk Institute for Biological Studies has developed a novel platform to study kidney diseases. This new platform should open new avenues for the future application of regenerative medical strategies to restore kidney function.

For the first time, the Salk researchers have generated three-dimensional kidney structures from human stem cells. These findings were reported November 17, 2013 in Nature Cell Biology, and they suggest new ways to study the development and diseases of the kidneys and to discover and test new drugs that target human kidney cells.

Scientists had created precursors of kidney cells using stem cells as recently as this past summer, but the Salk team was the first to coax human stem cells into forming three-dimensional cellular structures similar to those found in our kidneys.

“Attempts to differentiate human stem cells into renal cells have had limited success,” says senior study author Juan Carlos Izpisua Belmonte, a professor in Salk’s Gene Expression Laboratory and holder of the Roger Guillemin Chair. “We have developed a simple and efficient method that allows for the differentiation of human stem cells into well-organized 3D structures of the ureteric bud (UB), which later develops into the collecting duct system.”

The Salk findings demonstrate for the first time that pluripotent stem cells capable of differentiating into the many cells and tissue types that make up the body can be induced to differentiate into those cells found in the ureteric bud, which is an early developmental structure of the kidneys. Furthermore, these same cells can differentiate further into three-dimensional structures in organ cultures. Ureteric bud cells form the early stages of the human urinary and reproductive organs during development and later develop into a conduit for urine drainage from the kidneys. Izpisua Belmonte’s research group accomplished this with both human embryonic stem cells and induced pluripotent stem cells (iPSCs), human cells from the skin that have been reprogrammed into their pluripotent state.

Kidney development

After generating iPSCs that demonstrated pluripotent properties and were able to differentiate into mesoderm, the embryonic germ cell layer from which the kidneys develop, the Salk Institute team used growth factors known to be essential during the natural development of our kidneys to culture both iPSCs and embryonic stem cells.  The combination of signals from these growth factors, molecules that guide the differentiation of stem cells into specific tissues, committed the cells to become progenitors that exhibit clear characteristics of renal cells in only four days.

The researchers then guided these cells to further differentiate into organ structures similar to those found in the ureteric bud by culturing them with kidney cells from mice. This demonstrated that the mouse cells were able to provide the appropriate developmental cues to allow human stem cells to form three-dimensional structures of the kidney.

Izpisua Belmonte’s team also tested their protocol on iPSCs from a patient clinically diagnosed with polycystic kidney disease (PKD), a genetic disorder characterized by multiple, fluid-filled cysts that can lead to decreased kidney function and kidney failure. They found that their methodology could produce kidney structures from patient-derived iPSCs.

Polycystic kidneys
Polycystic kidneys

Because of the many clinical manifestations of the disease, neither gene- nor antibody-based therapies are realistic approaches for treating PKD. The Salk team’s technique might help circumvent this obstacle and provide a reliable platform for pharmaceutical companies and other investigators studying drug-based therapeutics for PKD and other kidney diseases.

“Our differentiation strategies represent the cornerstone of disease modeling and drug discovery studies,” says lead study author Ignacio Sancho-Martinez, a research associate in Izpisua Belmonte’s laboratory. “Our observations will help guide future studies on the precise cellular implications that PKD might play in the context of kidney development.”

Increased Flexibility in Induced Pluripotent Stem Cell Derivation Might Solve Tumor Concerns


Regenerative medicine depends on stem cells for the promises that it can potentially deliver to ailing patients. Training stem cells to repair injured tissues with custom-grown tissue substitutes and to replace dead cells are some of the goals of regenerative medicine. A major player in regenerative medicine is induced pluripotent stem cells (iPSCs), which are made from a patient’s own tissues. Because iPSCs are derived from a patient’s own cells, their chance of being rejected by the patient’s own immune system is rather low. Unfortunately, Shinya Yamanaka’s formula for making iPSCs, for which he was awarded last year’s Nobel Prize, utilizes a strict recipe that uses a precise combination of genes, some of which increase the risk of cancer risk, and, therefore, restricts their full potential for clinical application.

From left: Emmanuel Nivet and Juan Carlos Belmonte. Seated: Ignacio Sancho Martinez. (Source: Salk Institute for Biological Studies)
From left: Emmanuel Nivet and Juan Carlos Belmonte. Seated: Ignacio Sancho Martinez. (Source: Salk Institute for Biological Studies)

However, the laboratory Juan Carlos Izpisua Belmonte and his colleagues at the Salk Institute have published a paper in the journal Cell Stem Cell that shows that the recipe for iPSCs is much more versatile than originally thought. For the first time, Izpisua Belmonte and his colleague have replaced a gene that was once thought to be impossible to substitute in the production of iPSCs. This creates the potential for more flexible recipes that should speed the adoption of iPSCs for stem cell-based therapies.

Pluripotent stem cells come from two main sources. Embryonic stem cells (ESCs) are derived from early human blastocyst-stage embryos. The cells of the inner cell mass are extracted and these immature cells that have never differentiated into specific cell types, and are cultured, grown, and propagated to form an embryonic stem cell line. Secondly, induced pluripotent stem cells or iPSCs, are derived from mature cells that have been reprogrammed back into an undifferentiated state. In 2006 by Yamanaka introduced four different genes into a mature cell to reprogram the cell to pluripotency. This pluripotent cell can be cultured and grown into an iPSCs line. Because of Yamanaka’s initial success in iPSC production, most stem cell researchers adopted his recipe, even though variations on his protocol have been examined and used.

Izpisua Belmonte and his colleagues used a fresh approach for the derivation of iPSCs. They played around with the Yamanka protocol and in doing do discovered that pluripotency (the stem cell’s ability to differentiate into nearly any kind of adult cell) can also be programmed into adult cells by “balancing” the genes required for differentiation. What genes? Those genes that code for “lineage transcription factors,” which are proteins that direct stem cells to differentiate first into a particular cell lineage, or type, such as a blood cell versus a skin cell, and then finally into a specific cell, such as a white blood cell.

“Prior to this series of experiments, most researchers in the field started from the premise that they were trying to impose an ’embryonic-like’ state on mature cells,” says Izpisua Belmonte, who holds the Institute’s Roger Guillemin Chair. “Accordingly, major efforts had focused on the identification of factors that are typical of naturally occurring embryonic stem cells, which would allow or further enhance reprogramming.”

Despite these efforts, there seemed to be no way to determine through genetic identity alone that cells were pluripotent. Instead, pluripotency was routinely evaluated by functional assays. In other words, if it acts like a stem cell, it must be a stem cell.

That condition led the team to their key insight. “Pluripotency does not seem to represent a discrete cellular entity but rather a functional state elicited by a balance between opposite differentiation forces,” says Izpisua Belmonte.

Once they understood this, they realized the four extra genes weren’t necessary for pluripotency. Instead, adult cells could be reprogrammed by altering the balance of “lineage specifiers,” genes that were already in the cell that specified what type of adult tissue a cell might become.

“One of the implications of our findings is that stem cell identity is actually not fixed but rather an equilibrium that can be achieved by multiple different combinations of factors that are not necessarily typical of ESCs,” says Ignacio Sancho-Martinez, one of the first authors of the paper and a postdoctoral researcher in Izpisua Belmonte’s laboratory.

Izpisua Belmonte’s laboratory showed that more than seven additional genes can facilitate reprogramming adult cells to iPSCs. Most importantly, for the first time in human cells, they were able to replace a gene from the original recipe called Oct4, which had been replaced in mouse cells, but was still thought indispensable for the reprogramming of human cells. Their ability to replace it, as well as SOX2, another gene once thought essential that had never been replaced in combination with Oct4, demonstrated that stem cell development must be viewed in an entirely new way. In point of fact, Belmonte’s group showed that genes that specify mesendodermal lineage can replace OCT4 in human iPSC generation, and ectodermal lineage specifiers are able to replace SOX2 in hiPSC generation. Simultaneous replacement of OCT4 and SOX2 allows human cell reprogramming to iPSCs

“It was generally assumed that development led to cell/tissue specification by ‘opening’ certain differentiation doors,” says Emmanuel Nivet, a post-doctoral researcher in Izpisua Belmonte’s laboratory and co-first author of the paper, along with Sancho-Martinez and Nuria Montserrat of the Center for Regenerative Medicine in Barcelona, Spain.

Instead, the successful substitution of both Oct4 and SOX2 shows the opposite. “Pluripotency is like a room with all doors open, in which differentiation is accomplished by ‘closing’ doors,” Nivet says. “Inversely, reprogramming to pluripotency is accomplished by opening doors.”

This work should help to overcome one of the major hurdles in the widespread adoption of iPSC-based therapies; namely, that the original four genes used to reprogram stem cells had been implicated in cancer. “Recent studies in cancer, many of them done by my Salk colleagues, have shown molecular similarities between the proliferation of stem cells and cancer cells, so it is not surprising that oncogenes [genes linked to cancer] would be part of the iPSC recipe,” says Izpisua Belmonte.

With this new method, which allows for a customized recipe, the team hopes to push therapeutic research forward. “Since we have shown that it is possible to replace genes thought essential for reprogramming with several different genes that have not been previously involved in tumorigenesis, it is our hope that this study will enable iPSC research to more quickly translate into the clinic,” says Izpisua Belmonte.

Other researchers on the study were Tomoaki Hishida, Sachin Kumar, Yuriko Hishida, Yun Xia and Concepcion Rodriguez Esteban of the Salk Institute; Laia Miquel and Carme Cortina of the Center of Regenerative Medicine in Barcelona, Spain.