Author: Pallavi Penumetcha

Support cells have different roles in blood stem cell maintenance before and after stress

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Expression of pleiotrophin (green) in bone marrow blood vessels (red) and stromal cells (white) in normal mice (left), and in mice 24 hours after irradiation (right). UCLA Broad Stem Cell Research Center/Cell Stem Cell

A new study published in the journal Cell Stem Cell, reveals how different types of cells in the bone marrow are responsible for supporting blood stem cell maintenance before and after injury.

It was already well known in the field that two different cell types, namely endothelial cells (which line blood vessels) and stromal cells (which make up connective tissue, or tissue that provides structural support for any organ), are responsible for maintaining the population of blood stem cells in the bone marrow. However, how these cells and the molecules they secrete impact blood stem cell development and maintenance is not well understood.

Hematopoietic stem cells are responsible for generating the multiple different types of cells found in blood, from our oxygen carrying red blood cells to the many different types of white blood cells that make up our immune system.

Dr. John Chute’s group at UCLA had previously discovered that a molecule called pleiotrophin, or PTN, is important for promoting self-renewal of the blood stem cell population. They did not, however, understand which cells secrete this molecule and when.

To answer this question, the scientists developed mouse models that did not produce PTN in different types of bone marrow cells, such as endothelial cells and stromal cells. Surprisingly, they saw that the inability of stromal cells to produce PTN decreased the blood stem cell population, but deletion of PTN in endothelial cells did not affect the blood stem cell niche.

Even more interestingly, the researchers found that in animals that were subjected to an environmental stressor, in this case, radiation, the result was reversed: endothelial cell PTN was necessary for blood stem cell renewal, whereas stromal cell PTN was not. While an important part of the knowledge base for blood stem cell biology, the reason for this switch in PTN secretion at times of homeostasis and disease is still unknown.

As Dr. Chute states in a press release, this result could have important implications for cancer treatments such as radiation:

“It may be possible to administer modified, recombinant versions of pleiotrophin to patients to accelerate blood cell regeneration. This strategy also may apply to patients undergoing bone marrow transplants.”

Another important consideration to take away from this work is that animal models developed in the laboratory should take into account the possibility that blood stem cell maintenance and regeneration is distinctly controlled under healthy and disease state. In other words, cellular function in one state is not always indicative of its role in another state.

This work was partially funded by a CIRM Leadership Award.

 

 

For the first time, scientists entirely reprogram human skin cells to iPSCs using CRISPR

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CRISPR iPSC colony of human skin cells showing expression of SOX2 and TRA-1-60, markers of human embryonic pluripotent stem cells

Back in 2012, Shinya Yamanaka was awarded the Nobel Prize in Physiology or Medicine for his group’s identification of “Yamanaka Factors,” a group of genes that are capable of turning ordinary skin cells into induced pluripotentent stem cells (iPSCs) which have the ability to become any type of cell within the body. Discovery of iPSCs was, and has been, groundbreaking because it not only allows for unprecedented avenues to study human disease, but also has implications for using a patient’s own cells to treat a wide variety of diseases.

Recently, Timo Otonkoski’s group at the University of Helsinki along with Juha Kere’s group at the Karolinska Institutet and King’s College, London have found a way to program iPSCs from skin cells using CRISPR, a gene editing technology. Their approach allows for the induction, or turning on of iPSCs using the cells own DNA, instead of introducing the previously identified Yamanka Factors into cells of interest.

As detailed in their study, published in the journal Nature Communications, this is the first instance of mature human cells being completely reprogrammed into pluripotent cells using only CRISPR. Instead of using the canonical CRISPR system that allows the CAS9 protein (an enzyme that is able to cut DNA, thus rendering a gene of interest dysfunctional) to mutate any gene of interest, this group used a modified version of the CAS9 protein, which allows them to turn on or off the gene that CAS9 is targeted to.

The robustness of their approach lies in the researcher’s identification of a DNA sequence that is commonly found near genes involved in embryonic development. As CAS9 needs to be guided to genes of interest to do its job, identification of this common motif allows multiple genes associated with pluripotency to be activated in mature human skin cells, and greatly increased the efficiency and effectiveness of this approach.

In a press release, Dr. Otonkoski further highlights the novelty and viability of this approach:

“…Reprogramming based on activation of endogenous genes rather than overexpression of transgenes is…theoretically a more physiological way of controlling cell fate and may result in more normal cells…”

 

“Junk” DNA is development gold for the dividing embryo

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Single two-cell mouse embryos with nuclear LINE1 RNA labeled magenta – Credit Ramalho-Santos lab

The DNA in our cells provide the instructions to make proteins, the workhorses of our body. Yet less than 2% of the 3 billion base pairs (the structural units of DNA) in each of our cells are actually involved in protein production. The rest, termed non-coding DNA for not being involved in protein production, has roles in regulating genetic activity, but, largely, these genetic regions have remained a mystery causing some to mis-characterize it as “junk” DNA.

One of the largest components of these “junk” DNA regions are transposons, which make up 50% of the genome. Transposons are variable length DNA segments that are able to duplicate and re-insert themselves into different locations of the genome which is why they’re often called “jumping genes”.

Transposons have been implicated in diseases like cancer because of their ability to disrupt normal gene function depending on where the transposon inserts itself. Now, a CIRM-funded study in Miguel Ramalho-Santos’ laboratory at UCSF has found a developmental function for transposons in the dividing embryo. The report was published today in the Journal Cell.

Of the transposons identified in humans, LINE1 is the most common, composing 24% of the entire human genome. Many investigators in the field had observed that LINE1 is highly expressed in embryonic stem cells, which seemed paradoxical given that these pieces of DNA were previously thought to be either inert or harmful. Because this DNA was present at such high levels, the investigators decided to eliminate it from fertilized mouse embryos at the two-cell stage and observe how this affected development.

To their surprise, they found that the embryo was not able to progress beyond this stage. Further investigation revealed that LINE1, along with other proteins, is responsible for turning off the genetic program that maintains the two-cell state, thus allowing the embryo to further divide and develop.

Dr. Ramalho-Santos believes that this is a fine-tuned mechanism to ensure that the early stages of develop progress successfully. Because there are so many copies of LINE1 in the genome, even if one is not functional, it is likely that there will be functional back up, an important factor in ensuring early mistakes in embryo development do not occur.

In a press release, Dr. Ramalho-Santos states:

“We now think these early embryos are playing with fire but in a very calculated way. This could be a very robust mechanism for regulating development…I’m personally excited to continue exploring novel functions of these elements in development and disease.”

Timing is a critical factor in kidney development

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Through countless studies, it’s clear that genes and environmental factors are important for determining cellular identity. Now, a research team at the University of Southern California  (USC) have found that timing is another critical factor in determining cell fate during organ development.

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Developing human nephron, the filtering unit of the kidney. Image by Nils O. Lindstrom and Tracy Tran/McMahon Lab USC Stem Cell

In findings published in Development Cell, Dr. Andy McMahon’s group shows that development of the nephron, the filtering structure of the kidney, is acutely dependent on when cells arrive in that developmental region. Cells that arrive in the developing nephron early become part of the tubule, which is responsible for reabsorption of water and salt, whereas cells that arrive late become part of the glomerulus, the structure that is responsible for filtering blood.

The scientists verified that timing influenced cell identity with a combination of microscopy, which allowed them to follow particular cell types as they developed, and single-cell RNA sequencing, which allowed them to determine how gene expression changes in a population of cells.

In a press release, Dr. McMahon details the importance of these findings:

“By studying normal human nephron development, we’re gaining important information about how to replicate this intricate process in the laboratory. The hope is that laboratory-grown nephrons can be used to further study the process of development, screen potential therapies to treat disease, and eventually provide the building blocks to assemble functional kidneys for transplantation into patients.”

Understanding kidney development is crucial because approximately 30 million people suffer from chronic kidney disease and it is the ninth leading cause of death in the United States alone. Insights into the basics of kidney biology can provide important advances to develop novel therapeutics for this devastating condition.

CIRM funded study results in the first ever in utero stem cell transplant to treat alpha thalassemia

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Dr. Tippi MacKenzie (left) of UCSF Benioff Children’s Hospital San Francisco, visits with newborn Elianna and parents Nichelle Obar and Chris Constantino. Photo by Noah Berger

Imagine being able to cure a genetic disorder before a baby is even born. Thanks to a CIRM funded study, what would have been a mere dream a couple of years ago has become a reality.

Drs. Tippi MacKenzie and Juan Gonzalez Velez of the University of California San Francisco (UCSF) have successfully treated alpha thalassemia in Elianna Constantino, using stem cells from her mother’s bone marrow. Alpha thalassemia is part of a group of blood disorders that impairs the body’s ability to produce hemoglobin, the molecule that is responsible for transporting oxygen throughout the body on red blood cells. Present in approximately 5% of the population, alpha thalassemia is particularly prevalent among individuals of Asian heritage. Treatment options for this disease are severely limited, generally requiring multiple rounds of blood transfusions or a bone marrow transplant which requires immunosuppressive therapy. Normally, fetuses die in the womb or the pregnancy is aborted because of the poor prognosis.

The revolutionary treatment pioneered at UCSF involved isolating blood stem cells (cells that are capable of turning into all blood cell types) from the mother’s bone marrow and injecting these cells into Elianna’s bloodstream via the umbilical vein. The doctors were able to observe the development of healthy blood cells in the baby’s blood stream, allowing for efficient oxygen transport throughout the baby’s body. Because the cells were transplanted at the fetal stage, a time when the immune system is not fully developed, there was low risk of rejection and the transplant occurred without aggressive immunosuppressive therapy.

The baby was born healthy earlier this year and has been allowed to return home. While it is still too early to tell how effective this treatment will be in the long term, it is very encouraging that both the mother and baby have endured the treatment thus far.

In a press release, Dr. MacKenzie states:

“Her healthy birth suggests that fetal therapy is a viable option to offer to families with this diagnosis.”

The in utero stem cell transplant was performed as part of a clinical trial conducted at the UCSF Benioff Children’s Hospitals in San Francisco and Oakland. The trial is currently enrolling 10 pregnant women to test the safety and effectiveness of this treatment over a wider population.

If successful, this type of treatment is particularly exciting because it could be expanded to other types of hereditary blood disorders such as sickle cell anemia and hemophilia.

 

 

 

Making stem cell-derived liver cells to study fatty liver disease

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Non-alcoholic fatty liver disease (NAFLD) affects approximately 30% of the population, with that number increasing to 75% in obese individuals. Shockingly, the number of cases is expected to increase 21% by the year 2030 in the United States alone.

liver_fattyliverNAFLD refers to a broad range of liver conditions, which are all characterized by abnormally high levels of fat deposits in the livers of people who do not drink excessive amounts of alcohol. While not always fatal, NAFLD can lead to liver cirrhosis, or extensive scaring of the liver tissue. Cirrhosis, in turn, can cause life-threatening conditions such as liver cancer or liver failure. Whether or not N

AFLD will lead to extensive liver damage is not well understood and the primary therapeutic option is weight loss with no FDA-approved drug options. The projected increase in NALD cases combined with the poor treatment options makes this disease a significant public health burden.

Studying NALD can be quite complicated because the liver is complex organ made up of multiple different cell types. Investigators at the University of Edinburgh have simplified some of this complexity by figuring out a way to generate liver cells in a dish.

In studies published in the Philosophical Transactions of the Royal Society B, these scientists used human embryonic stem cells to generate hepatocyte-like cells (HLCs), or cells that are highly similar to liver cells isolated from humans. When exposed to fatty acids, they saw that the HLCs exhibited hallmarks of NAFLD, such as fat accumulation in liver cells, and changes in gene expression that are indicative of NAFLD.

In a press release, Dr. David Hay, one of the two senior investigators of this study, states:

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Dr. David Hay

“Our ability to generate human hepatocytes from stem cells, using semi-automated procedures, allows us to study the mechanisms of human liver disease in a dish and at scale.”

 

This approach is particularly valuable because it would replace the need to use cancer cell lines for this type of work. While valuable for many reasons, research done in cancer cells lines can be difficult to draw therapeutic conclusions from, because cell lines have significant genetic alternations from normal cells. Generating liver cells from human stem cells provides an important tool for high throughput screening of medically relevant therapies for NALD.

 

New findings about muscle stem cells reveals the potential for growing replacement organs

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Chrissa Kioussi’s group at Oregon State University has made exciting advances in further unraveling the scientific mysteries of stem cells. In work detailed in Scientific Reports, this group found that muscle-specific stem cells actually have the ability to make multiple different cell types.

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Pumping up our knowledge about muscle stem cells

Initially, this group was interested in understanding how gene expression changes during embryonic development of skeletal muscle. To understand this process, they labeled muscle stem cells with a kind of fluorescent dye, called GFP, which allowed them to isolate these cells at different stages of development.  Once isolated, they determined what genes were being expressed by RNA sequencing. Surprisingly, they found that in addition to genes involved in muscle formation, they also identified activation of genes involved in the blood, nervous, immune and skeletal systems.

This work is particularly exciting, because it suggests the existence of stem cell “pockets,” or stem cells that are capable of not only making a specific cell type, but an entire organ system.

In a press release, Dr. Kioussi said:

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Chrissa Kioussi, PhD

“That cell populations can give rise to so many different cell types, we can use it at the development stage and allow it to become something else over time… We can identify these cells and be able to generate not one but four different organs from them — this is a prelude to making body parts in a lab.” 

This study is particularly exciting because it gives more credence to the idea that entire limbs can be reconstructed from a small group of stem cells. Such advances could have enormous meaning for individuals who have lost body parts due to amputation or disease.

Using biological “codes” to generate neurons in a dish

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BrainWavesInvestigators at the Scripps Research Institute are making brain waves in the field of neuroscience. Until now, neuroscience research has largely relied on a variety of animal models to understand the complexities of various brain or neuronal diseases. While beneficial for many reasons, animal models do not always allow scientists to understand the precise mechanism of neuronal dysfunction, and studies done in animals can often be difficult to translate to humans. The work done by Kristin Baldwin’s group, however, is revolutionizing this field by trying to re-create this complexity in a dish.

One of the primary hurdles that scientists have had to overcome in studying neuronal diseases, is the impressive diversity of neuronal cell types that exist. The exact number of neuronal subtypes is unknown, but scientists estimate the number to be in the hundreds.

While neurons have many similarities, such as the ability to receive and send information via chemical cues, they are also distinctly specialized. For example, some neurons are involved in sensing the external environment, whereas others may be involved in helping our muscles move. Effective medical treatment for neuronal diseases is contingent on scientists being able to understand how and why specific neuronal subtypes do not function properly.

In a study in the journal Nature, partially funded by CIRM, the scientists used pairs of transcription factors (proteins that affect gene expression and cell identity), to turn skin stem cells into neurons. These cells both physically looked like neurons and exhibited characteristic neuronal properties, such as action potential generation (the ability to conduct electrical impulses). Surprisingly, the team also found that they were able to generate neurons that had unique and specialized features based on the transcription factors pairs used.

The ability to create neuronal diversity using this method indicates that this protocol could be used to recapitulate neuronal diversity outside of the body. In a press release, Dr. Baldwin states:

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Kristin Baldwin, PhD

“Now we can be better genome detectives. Building up a database of these codes [transcription factors] and the types of neurons they produce can help us directly link genomic studies of human brain disease to a molecular understanding of what goes wrong with neurons, which is the key to finding and targeting treatments.”

These findings provide an exciting and promising tool to more effectively study the complexities of neuronal disease. The investigators of this study have made their results available on a free platform called BioGPS in the hopes that multiple labs will delve into the wealth of information they have opened up. Hopefully, this system will lead to more rapid drug discovery for disease like autism and Alzheimer’s

Coming up with a stem cell FIX for a life-threatening blood disorder

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Hemophilia

A promising new treatment option for hemophiliacs is in the works at the Salk Institute for Biological Sciences. Patients with Hemophilia B experience uncontrolled, and sometimes life threatening, bleeding due to loss or improper function of Factor IX (FIX), a protein involved in blood clotting. There is no cure for the disease and patients rely on routine infusions of FIX to prevent excessive blood loss. As you can imagine, this treatment regimen is both time consuming and expensive, while also becoming less effective over time.

Salk researchers, partially funded by CIRM, aimed to develop a more long-term solution for this devastating disease by using the body’s own cells to fix the problem.

In the study, published in the journal Cell Reports, They harvested blood cells from hemophiliacs and turned them into iPSCs (induced pluripotent stem cells), which are able to turn into any cell type. Using gene editing, they repaired the iPSCs so they could produce FIX and then turned the iPSCs into liver cells, the cell type that naturally produces FIX in healthy individuals.

One step therapy

To test whether these FIX-producing liver cells were able to reduce excess blood loss, the scientists injected the repaired human cells into a hemophiliac mouse. The results were very encouraging; they saw a greater than two-fold increase in clotting efficiency in the mice, reaching about a quarter of normal activity. This is particularly promising because other studies showed that increasing FIX activity to this level in hemophiliac humans significantly reduces bleeding rates. On top of that they also observed that these cells were able to survive and produce FIX for up to a year in the mice.

In a news release Suvasini Ramaswamy, the first author of the paper, said this method could eliminate the need for multiple treatments, as well as avoiding the immunosuppressive therapy that would be required for a whole liver transplant.

“The appeal of a cell-based approach is that you minimize the number of treatments that a patient needs. Rather than constant injections, you can do this in one shot.”

While these results provide an exciting new avenue in hemophilia treatment, there is still much more work that needs to be done before this type of treatment can be used in humans. This approach, however, is particularly exciting because it provides an important proof of principle that combining stem cell reprogramming with genetic engineering can lead to life-changing breakthroughs for treating genetic diseases that are not currently curable.