Stem Cell Roundup: Knowing the nose, stem cell stress and cell fate math.

The Stem Cellar’s Image of the Week.
Our favorite image this week, comes to us from researchers at Washington University School of Medicine in St. Louis. Looking like a psychedelic Rorschach test, the fluorescence microscopy depicts mouse olfactory epithelium (in green), a sheet of tissue that develops in the nose. The team identified a new stem cell type that controls the growth of this tissue. New insights from the study of these cells could help the team better understand why some animals, like dogs, have a far superior sense of smell than humans.

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Peering into the nasal cavity of a mouse. Olfactory epithelium is indicated by green. Image credit: Lu Yang, Washington University School of Medicine in St. Louis.

A Washington U. press release provides more details about this fascinating study which appears in Developmental Cell.

How stress affects blood-forming stem cells.
Stress affects all of us in different ways. Some people handle it well. Some crack up and become nervous wrecks. So, perhaps it shouldn’t come as a huge surprise that stress also affects some stem cells. What is a pleasant surprise is that knowing this could help people undergoing cancer therapy or bone marrow transplants.

First a bit of background. Hematopoietic, or blood-forming stem cells (HSCs) come from bone marrow and are supported by other cells that secrete growth factors, including one called pleiotrophin or PTN. While researchers knew PTN was present in bone marrow they weren’t sure precisely what role it played.

So, researchers at UCLA set out to discover what PTN did.

In a CIRM-funded study they took mice that lacked PTN in endothelial cells – these line the blood vessels – or in their stromal cells – which make up the connective tissue. They found that a lack of PTN in stromal cells caused a lack of blood stem cells, but a lack of PTN in endothelial cells had no impact.

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Expression of pleiotrophin (green) in bone marrow blood vessels (red) and stromal cells (white) is shown in normal mice (left) and in mice at 24 hours following irradiation (right). Image credit: UCLA

However, as Dr. John Chute explained in a news release, when they stressed the cells, by exposing them to radiation, they found something very different:

“The surprising finding was that pleiotrophin from stromal cells was not necessary for blood stem cell regeneration following irradiation — but pleiotrophin from endothelial cells was necessary.”

In other words, during normal times the stem cells rely on PTN from stromal cells, but after stress they depend on PTN from endothelial cells.

Dr. Chute says, because treatments like chemotherapy and radiation deplete bone marrow stem cells, this finding could have real-world implications for patients.

“These therapies for cancer patients suppress our blood cell systems over time. 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.”

The study appears in the journal Cell Stem Cell.

Predicting the fate of cells with math
Researchers at Harvard Medical School and the Karolinska Institutet in Sweden reported this week that they have devised a mathematical model that can predict the fate of stem cells in the brain.

It may sound like science-fiction but the accomplished the feat by tracking changes in messenger RNA (mRNA), the genetic molecule that translates our DNA code into instructions for building proteins. As a brain stem cell begins specializing into specific cell types, hundreds of genes get turns on and off, which is observed by the rate of changes in mRNA productions.

The team built their predictive model by measuring these changes. In a press release, co-senior author, Harvard professor Peter Kharchenko, described this process using a great analogy:

“Estimating RNA velocity—or the rate of RNA change over time—is akin to observing the cooks in a restaurant kitchen as they line up the ingredients to figure out what dishes they’ll be serving up next.”

The team verified their mathematical model by inputting other data that was not use in constructing the model. Karolinkska Institutet professor, Sten Linnarsson, the other co-senior author on the study, described how such a model could be applied to human biomedical research:

“RNA velocity shows in detail how neurons and other cells acquire their specific functions as the brain develops and matures. We’re especially excited that this new method promises to help reveal how brains normally develop, but also to provide clues as to what goes wrong in human disorders of brain development, such as schizophrenia and autism.”

The study appears in the journal Nature.

Bioengineers Build 3D Model of Human Heart Ventricle

 

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Photo courtesy of Luke MacQueen/Disease Biophysics Group/Harvard SEAS.

After more than a decade, scientists at Harvard University finally made a breakthrough in their efforts to create a heart. According to a study published in Nature Biomedical Engineering, the researchers successfully bioengineered a three-dimensional model of a human left heart ventricle. This important development brings them one step closer to their goal, creating a life-like model of a heart which could ultimately help scientists study heart disease, test drugs and develop patient-specific treatments for other heart conditions such as arrhythmia.

The key to building a functional ventricle is recreating the tissue’s unique structure. In human hearts, myocardial fibers act as a scaffold, guiding brick-shaped heart cells to align and assemble end-to-end, forming a hollow, cone-shaped structure. When the heart beats, the cells expand and contract like an accordion.

To make the ventricle, the researchers used a combination of biodegradable polyester and gelatin fibers that were collected on a rotating collector shaped like a bullet. Because the collector is spinning, all of the fibers align in the same direction.

The tissue is engineered with a nanofiber scaffold seeded with human heart cells. The scaffold acts like a 3D template, guiding the cells and their assembly into ventricle chambers that beat in time with each other. This allowed researchers to study heart function in the lab, using many of the same tools used in the clinic, including pressure-volume loops and ultrasound.

After building the scaffold, the researchers cultured the ventricle with either rat muscle cells from rats or human heart muscle cells. Within three to five days, a thin wall of tissue covered the scaffold and cells were beating in synch. From there, researchers could control and monitor different aspects of the ventricle, such as pressure and volume of the beating.

To test the heart, the researchers exposed the tissue to isoproterenol, a drug similar to adrenaline, and measured as the beat-rate increased just as it would in human and rat hearts. The researchers also poked holes in the ventricle to mimic a heart attack and studied the effects in a petri dish. Using human heart muscle cells from induced stem cells, the researchers were even able to culture the ventricles for 6 months and measure stable pressure-volume loops.

“The long-term objective of this project is to replace or supplement animal models with human models and especially patient-specific human models,” said Luke MacQueen, Ph.D., first author of the study and postdoctoral fellow at the Wyss Institute and SEAS. “In the future, patient stem cells could be collected and used to build tissue models that replicate some of the features of their whole organ.”

While the applications for regenerative cardiovascular medicine are wide and varied, this advancement in their research is a step toward more accurate models of actual patient diseases.

In the future, we could see patient stem cells collected and used to build tissue models that replicate some or even all of the features of their entire organ.

A scalable, clinic-friendly recipe for converting skin cells to muscle cells

Way back in 1987, about two decades before Shinya Yamanaka would go on to identify four proteins that can reprogram skin cells into induced pluripotent stem cells (iPSCs), Harold Weintraub’s lab identified the first “master control” protein, MyoD, which can directly convert a skin cell into a muscle cell. Though MyoD opened up new approaches for teasing out the molecular mechanisms of a cell’s identity, it did not produce therapeutic paths for replacing muscle damaged by disease and injury.

That’s because MyoD-generated muscle cells are not amenable to a clinical setting. For a cell therapy to be viable, you need to manufacture large amounts of your product to treat many people. But these MyoD cells do not grow well enough to be effective to serve as a cell replacement therapy. Generating iPSC-derived muscle cells provides the potential of overcoming this limitation but the capacity of the embryonic stem cell-like iPSC for unlimited growth carries a risk of forming tumors after the transplanting iPSC-derived cell therapies into the muscle.

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This image shows iMPCs stained for markers of muscle stem, progenitor and differentiated cells. iMPCs recapitulate muscle differentiation in a dish. Credit: Ori Bar-Nur and Mattia Gerli

A recent study in Stem Cell Reports, by Konrad Hochedlinger’s lab at Massachusetts General Hospital and the Harvard Stem Cell Institute, may provide a work around. The team came up with a recipe that calls for the temporary activation of MyoD in mouse skin cells, along with the addition of three molecules that boost cell reprogramming. The result? Cells they dubbed induced myogenic progenitor cells, or iMPCs, that can make self-sustaining copies of themselves and can be scaled up for manufacturing purposes. On top of that, they show that these iMPCs carry the hallmarks of muscle stem cells and generate muscle fibers when transplanted into mice with leg injuries without signs of tumor formation.

A lot of work still remains to be done, like confirming that these iMPCs truly have the same characteristics as muscle stem cells. But if everything pans out, the potential applications for people suffering from various muscle disorders and injuries is very exciting, as co-first author Mattia FM Gerli, PhD points out in a press release:

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Mattia FM Gerli, PhD

“Patient-specific iMPCs could be used for personalized medicine by treating patients with their own genetically matched cells. If disease-causing mutations are known, as is the case in many muscular dystrophies, one could in principle repair the mutation in iMPCs prior to transplantation of the corrected cells back into the patient.”

Stem Cell Round: Improving memory, building up “good” fat, nanomedicine

Stem Cell Photo of the Week

roundup03618In honor of brain awareness week, our featured stem cell photo is of the brain! Scientists at the Massachusetts General Hospital and Harvard Stem Cell Institute identified a genetic switch that could potentially improve memory during aging and symptoms of PTSD. Shown in this picture are dentate gyrus cells (DGC) (green) and CA3 interneurons (red) located in the memory-forming area of the brain known as the hippocampus. By reducing the levels of a protein called abLIM3 in the DGCs of older mice, the researchers were able to boost the connections between DGCs and CA3 cells, which resulted in an improvement in the memories of the mice. The team believes that targeting this protein in aging adults could be a potential strategy for improving memory and treating patients with post-traumatic stress disorder (PTSD). You can read more about this study in The Harvard Gazette.

New target for obesity.
Fat cells typically get a bad rap, but there’s actually a type of fat cell that is considered “healthier” than others. Unlike white fat cells that store calories in the form of energy, brown fat cells are packed with mitochondria that burn energy and produce heat. Babies have brown fat, so they can regulate their body temperature to stay warm. Adults also have some brown fat, but as we get older, our stores are slowly depleted.

In the fight against obesity, scientists are looking for ways to increase the amount of brown fat and decrease the amount of white fat in the body. This week, CIRM-funded researchers from the Salk Institute identified a molecule called ERRg that gives brown fat its ability to burn energy. Their findings, published in Cell Reports, offer a new target for obesity and obesity-related diseases like diabetes and fatty liver disease.

The team discovered that brown fat cells produce the ERRg molecule while white fat cells do not. Additionally, mice that couldn’t make the ERRg weren’t able to regulate their body temperature in cold environments. The team concluded in a news release that ERRg is “involved in protection against the cold and underpins brown fat identity.” In future studies, the researchers plan to activate ERRg in white fat cells to see if this will shift their identity to be more similar to brown fat cells.

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Mice that lack ERR aren’t able to regulate their body temperature and are much colder (right) than normal mice (left). (Image credit Salk Institute)

Tale of two nanomedicine stories: making gene therapies more efficient with a bit of caution (Todd Dubnicoff).
This week, the worlds of gene therapy, stem cells and nanomedicine converged for not one, but two published reports in the journal American Chemistry Society NANO.

The first paper described the development of so-called nanospears – tiny splinter-like magnetized structures with a diameter 5000 times smaller than a strand of human hair – that could make gene therapy more efficient and less costly. Gene therapy is an exciting treatment strategy because it tackles genetic diseases at their source by repairing or replacing faulty DNA sequences in cells. In fact, several CIRM-funded clinical trials apply this method in stem cells to treat immune disorders, like severe combined immunodeficiency and sickle cell anemia.

This technique requires getting DNA into diseased cells to make the genetic fix. Current methods have low efficiency and can be very damaging to the cells. The UCLA research team behind the study tested the nanospear-delivery of DNA encoding a gene that causes cells to glow green. They showed that 80 percent of treated cells did indeed glow green, a much higher efficiency than standard methods. And probably due to their miniscule size, the nanospears were gentle with 90 percent of the green glowing cells surviving the procedure.

As Steve Jonas, one of the team leads on the project mentions in a press release, this new method could bode well for future recipients of gene therapies:

“The biggest barrier right now to getting either a gene therapy or an immunotherapy to patients is the processing time. New methods to generate these therapies more quickly, effectively and safely are going to accelerate innovation in this research area and bring these therapies to patients sooner, and that’s the goal we all have.”

While the study above describes an innovative nanomedicine technology, the next paper inserts a note of caution about how experiments in this field should be set up and analyzed. A collaborative team from Brigham and Women’s Hospital, Stanford University, UC Berkeley and McGill University wanted to get to the bottom of why the many advances in nanomedicine had not ultimately led to many new clinical trials. They set out looking for elements within experiments that could affect the uptake of nanoparticles into cells, something that would muck up the interpretation of results.

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imaging of female human amniotic stem cells incubated with nanoparticles demonstrated a significant increase in uptake compared to male cells. (Green dots: nanoparticles; red: cell staining; blue: nuclei) Credit: Morteza Mahmoudi, Brigham and Women’s Hospital.

In this study, they report that the sex of cells has a surprising, noticeable impact on nanoparticle uptake. Nanoparticles were incubated with human amniotic stem cells derived from either males or females. The team showed that the female cells took up the nanoparticles much more readily than the male cells.  Morteza Mahmoudi, PhD, one of the authors on the paper, explained the implications of these results in a press release:

“These differences could have a critical impact on the administration of nanoparticles. If nanoparticles are carrying a drug to deliver [including gene therapies], different uptake could mean different therapeutic efficacy and other important differences, such as safety, in clinical data.”

 

Stem Cell Tools: Helping Scientists Model Complex Diseases

This blog is part of the Month of CIRM series and the first of two blogs focused on how CIRM-funded infrastructure initiatives are developing useful tools to advance stem cell research. 

Human stem cells are powerful tools for studying human disease.  Animal models like mice have been and continue to be important for studying physiological systems, but they are still different than human systems.  Other types of human cells studied in the lab often are isolated from cancers or modified to multiply indefinitely.  However, the genetic DNA blueprint of these modified cells are irreparably altered from the normal tissues that they came from.

Human pluripotent stem cells are unique in that they can be grown in the lab and turned into any type of normal cell in the body.  Many scientists now believe that creating such stem cell lines from patients and developing ‘disease-in-a-dish’ models will provide important insights that will lead to treatments for the disorders from which they came.  Challenges still remain to develop these models to their fullest potential.  Because the genetics underlying human disease is complex, detailed genetic information about each stem cell line, as well as a large number of lines  to represent the genetic variability between patients will be needed to make progress.

To address this need, CIRM funded the creation of the world’s largest induced pluripotent stem cell bank, which we call the CIRM iPSC Repository.  iPSCs are similar to embryonic stem cells in that they can develop into any cell type found in the body, but they differ in how they are derived. Scientists can take human skin or blood cells and genetically reprogram them into iPSCs that have the same genetic makeup, including any disease-causing mutations, as the person from which the original cells were taken. Embryonic stem cells, on the other hand, are derived from left over embryos donated by couples undergoing in vitro fertilization (IVF) treatments.

The CIRM iPSC Repository was established to harness the power of iPSCs as tools for disease modeling and drug discovery. The Repository currently offers scientists around the world access to over 1500 high-quality iPSC lines covering diseases of the brain, heart, liver, lung, and eye, and the collection will eventually hold over 3000 lines.  All iPSC lines are linked to publicly-accessible demographic and clinical information.

Making the Cell Lines

Making the iPSC Repository was no easy task – it took a village of doctors, scientists, patients and healthy volunteers. First, clinicians across California collected blood and skin samples from over 2800 people including individuals with common diseases, rare diseases and healthy controls. CIRM then awarded a grant to Cellular Dynamics International to create iPSC lines from these donors, and a second grant to the Coriell Institute to store and distribute the lines to interested labs around the world. Creating such a large number of lines in a single concerted effort has been a challenging logistical feat that has taken almost five years and is projected to finish in early 2018.

Joachim Hallmayer

We spoke with one of the tissue collectors, a scientist named Dr. Joachim Hallmayer at Stanford University, about the effort it took to obtain tissue samples for the Repository. Hallmayer is a Professor of Psychiatry and Behavioral Sciences at Stanford who studies Autism Spectrum Disorder (ASD) in children. With funding from a CIRM Tissue Collection for Disease Modeling award, Hallmayer collected tissue samples from children with ASD and children with normal development. His efforts resulted in the 164 ASD and 134 control samples for the Repository.

Hallmayer emphasized that each sample donation required significant attention and education from the clinical staff to the donor.  Communicating with patients and walking them through the consent process for donating their tissue for this purpose is an extremely important issue that is often overlooked. “Conveying information about the tissue collection process to patients takes a lot of time. However, deconstructing the consent process is essential for patients to understand what they are donating and why,” explained Hallmayer.

Now that the ASD lines are available, Hallmayer and his colleague Dr. Ruth O’Hara are formulating a plan to model ASD in a dish by differentiating the iPSC lines into neurons affected by this disorder. Says O’Hara:

Ruth O’Hara

“While the examination of live tissue from other organ systems has become increasingly viable, examining live neurons from patients with brain disorders has simply not been possible. Using iPSC-derived neurons, for the first time we can study live nerve cells from actual patients and compare these cells to those from humans without the disorder.”

Using iPSCs to Model Psychiatric Disorders

Ultimately, the goal of iPSCs for modeling disease is to identify mechanisms and therapeutic targets for the disorders that they represent.  Studying a disease through a single iPSC line may not shed enough light on that disorder.  Just as people have diverse traits, the way that a disease can affect individuals is also diverse.  Studying large numbers of lines in a time and cost-efficient manner that represent these diverse traits, and the genetic causes that underlie them, can be a powerful method to understand and address diseases.

 To leverage the iPSC collection for this purpose, CIRM and a group of scientists at the Broad Institute’s Stanley Center for Psychiatric Research and Harvard University have entered into a collaboration to study psychiatric disorders such as ASD.  Because the donor samples were collected on the basis of clinical information, the genetic information about what caused their disease remains unknown.  Therefore, the Stanley Center will embark on whole genome sequencing (WGS) of hundreds of lines from the CIRM iPSC repository. Adding donor WGS sequence information to the CIRM repository will significantly increase its value, as scientists will be able to use DNA sequence information to select the ideal lines for disease modeling and therapeutic discovery efforts. The collaboration aims to identify the genes that shape neuronal phenotypes in iPSC-derived neurons from patients with psychiatric disorders.

“A central challenge today is to discover how inherited genetic variation gives rise to functional variation in the properties of neurons and other cells,” said Steven McCarroll, Director of Genetics at the Broad Institute’s Stanley Center for Psychiatric Research, and associate professor at Harvard Medical School’s Department of Genetics. “We hope with the analysis of cells from very large numbers of genetically diverse individuals will begin to address longstanding problems at the interface of human genetics and biology.”

iPSC derived neurons growing in a dish. (Image courtesy of Ralda Nehme, Research Scientist at the Broad Institute).

Such efforts require technologies such as Drop-seq, developed in the McCarroll lab, where genome-wide expression of thousands of separate cells can be analyzed in one experiment. These efforts also rely on scaling functional analysis of stem cell-based disease models, a vexing bottleneck for the field. “The CIRM iPSC Repository is the largest and most ambitious of its kind”, said Kevin Eggan, Professor of Stem Cell and Regenerative Biology at Harvard University, and Director of Stem Cell Biology at the Broad Institute’s Stanley Center for Psychiatric Research. Efforts underway in Dr. Eggan’s lab are directed at developing approaches to analyze large numbers of stem cell lines in parallel.

“The scale of the CIRM iPSC collection will allow us to investigate how variation that is common among many of us predisposes certain individuals to major mental illnesses such as autism and other neurodevelopmental disorders. We are incredibly excited about entering this long-term collaboration.”

Members of the Eggan and McCarroll labs at the Broad Institute’s Stanley Center for Psychiatric Research. (Image courtesy of Kiki Lilliehook)

From Cell Lines to Data

It’s clear from these stories, that the iPSC Repository is a unique and powerful tool for the stem cell research community. But for the rewards to be truly reaped, more tools are needed that will help scientists study these cell lines. This is where the CIRM Genomics Initiative comes into play.

Be sure to read Part 2 of our Stem Cell Tools series tomorrow to find out how our Genomics Initiative is funding the development of genomic and bioinformatics tools that will allow scientists to decipher complex stem cell data all the way from mapping the developmental states of cells to predicting the accuracy of stem cell-based models.

This blog was written in collaboration with Dr. Kiki Lilliehook, the Manager of the Stem Cell Program at the Stanley Center for Psychiatric Research at the Broad Institute in Cambridge, Massachusetts.

Cancer-causing mutations in blood stem cells may also link to heart disease

Whether we read about it in the news or hear it from our doctor, when we think about the causes of heart disease it’s usually some combination of inheriting bad genes from our parents and making poor life style choices like smoking or eating a diet high in fat and cholesterol. But in a fascinating research published yesterday in the New England Journal of Medicine, scientists show evidence that in some people, heart disease may develop much in the same way that a blood cancer does; that is, through a gradual, lifetime accumulation of mutations in hematopoietic cells, or blood stem cells.

This surprising discovery began as a project, published in 2014, aimed at early detection of blood cancers in the general population. This earlier study focused on the line of evidence that cells don’t become cancerous overnight but rather progress slowly as we age. So, in the case of a blood cancer, or leukemia, a blood stem cell can acquire a mutation that transforms the cell into a pre-cancerous state. When that stem cell multiplies it creates “clones” of the blood stem cell that had the cancer-initiating mutation. It’s only after additional genetic insults that these stem cells become full blown cancers.

The research team, composed of scientists from Brigham and Women’s Hospital as well as the Broad Institute of Harvard and MIT, examined DNA sequences from blood samples of over 17,000 people who didn’t have blood cancer. They analyzed these samples, specifically looking at 160 genes that are often mutated in blood cancer. The results from the 2014 study showed that mutations in these genes in people 40 years and under were few and far between. Interestingly, the frequency noticeably increased in older folks with those 10% over 70 years of age carrying the mutations.

Most of these so-called “clonal hematopoiesis of indeterminate potential”, or CHIP, mutations occurred in three genes called DNMT3A, TET2, and ASXL1. While these mutations were indeed associated with a 10-fold higher risk of blood cancer, the team also saw an unexpected correlation: people with these mutations had a 40% higher overall risk of dying due to other causes compared to those who did not carry the mutations. They pinpointed heart disease as one primary cause of the increased mortality risk.

The current follow-up study not only sought to confirm this correlation between the mutations and heart disease but also show the mutations cause the increased risk. This time around, the team looked for the mutations in a group of four different populations totaling over 8000 people. Again, they saw a correlation between the mutations and the risk of heart disease or a heart attack later in life. One of the team leads, Dr. Sekar Kathiresan from the Broad Institute, talked about his team’s reaction to these results in a Time Magazine interview:

Sekar Kathiresan, Photo: Broad Institute

“We were fully expecting not to find anything here. But the odds of having an early heart attack are four-fold higher among younger people with CHIP mutations.”

 

To show a causal link, they turned to mouse studies. They collected bone marrow stem cells from mice engineered to lack Tet2, one of the three genes that when mutated had been associated with increased risk of heart disease. The bone marrow cells were then transplanted into mice which are prone to have increased blood cholesterol and symptoms of heart disease. The presence of these cells that lacked Tet2 led to increased hardening of major arteries – a precursor to clogged blood vessels, heart disease and heart attacks – compared to mice that received normal bone marrow cells.

Though more work remains, Kathiresan thinks these current results offer some tantalizing therapeutic possibilities:

“This is a totally different type of risk factor than hypertension or hypercholestserolemia [high blood cholesterol] or smoking. And since it’s a totally different risk factor that works through a different mechanism, it may lead to new treatment opportunities very different from the ones we have for heart disease at present.”

Kidney Disease: There’s an Organ-on-a-Chip for That

“There’s an app for that” is a well-known phrase trademarked by Apple to promote how users can do almost anything they do on a computer on their mobile phone. Apps are so deeply ingrained in everyday life that it’s hard for some people to imagine living without them. (I know I’d be lost without google maps or my Next Bus app!)

An estimated 2.2 million mobile apps exist for iPhones. Imagine if this multitude of apps were instead the number of stem cell models available for scientists to study human biology and disease. Scientists dream of the day when they can respond to questions about any disease and say, “there’s a model for that.” However, a future where every individual or disease has its own personalized stem cell line is still far away.

In the meantime, scientists are continuing to generate stem cell-based technologies that answer important questions about how our tissues and organs function and what happens when they are affected by disease. One strategy involves growing human stem cells on microchips and developing them into miniature organ systems that function like the organs in our bodies.

Kidney-on-a-chip

A group of scientists from Harvard’s Wyss Institute are using organ-on-a-chip technology to model a structure in the human kidney, called a glomerulus, that’s essential for filtering the body’s blood. It’s made up of a meshwork of blood vessels called capillaries that remove waste, toxic products, and excess fluid from the blood by depositing them into the urine.

The glomerulus also contains cells called podocytes that wrap around the capillaries and leave thin slits for blood to filter through. Diseases that affect podocytes or the glomerulus structure can cause kidney failure early or later in life, which is why the Harvard team was so interested to model this structure using their microchip technology.

They developed a method to mature human pluripotent stem cells into podocytes by engineering an environment similar to that of a real kidney on a microchip. Using a combination of kidney-specific factors and extracellular matrix molecules, which form a supportive environment for cells within tissues and organs, the team generated mature podocytes from human stem cells in three weeks. Their study was published in Nature Biomedical Engineering and was led by Dr. Donald Ingber, Founding Director of the Wyss Institute.

3D rendering of the glomerulus-on-a-chip derived from human stem cells. (Wyss Institute at Harvard University)

First author, Samaira Musah, explained how their glomerulus-on-a-chip works in a news release,

“Our method not only uses soluble factors that guide kidney development in the embryo, but, by growing and differentiating stem cells on extracellular matrix components that are also contained in the membrane separating the glomerular blood and urinary systems, we more closely mimic the natural environment in which podocytes are induced and mature. We even succeeded in inducing much of this differentiation process within a channel of the microfluidic chip, where by applying cyclical motions that mimic the rhythmic deformations living glomeruli experience due to pressure pulses generated by each heartbeat, we achieve even greater maturation efficiencies.”

Over 90% of stem cells successfully developed into functional podocytes that could properly filter blood by selectively filtering different blood proteins. The podocytes also were susceptible to a chemotherapy drug called doxorubicin, proving that they are suitable for modeling the effects of drug toxicity on kidneys.

Kidney podocyte derived from human stem cells. (Wyss Institute)

Ingber highlighted the potential applications of their glomerulus-on-a-chip technology,

Donald Ingber, Wyss Institute

“The development of a functional human kidney glomerulus chip opens up an entire new experimental path to investigate kidney biology, carry out highly personalized modeling of kidney diseases and drug toxicities, and the stem cell-derived kidney podocytes we developed could even offer a new injectable cell therapy approach for regenerative medicine in patients with life-threatening glomerulopathies in the future.”

There’s an organ-on-a-chip for that!

The Wyss Institute team has developed other organ-on-chips including lungs, intestine, skin and bone marrow. These miniature human systems are powerful tools that scientists hope will “revolutionize drug development, disease modeling and personalized medicine” by reducing the cost of research and the reliance on animal models according to the Wyss Institute technology website.

What started out as a microengineering experiment in Ingber’s lab a few years ago is now transforming into a technology “that is now poised to have a major impact on society” Ingber further explained. If organs-on-chips live up to these expectations, you might one day hear a scientist say, “Don’t worry, there’s an organ-on-a-chip for that!”


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Stem cell stories that caught our eye: better ovarian cancer drugs, creating inner ear tissue, small fish big splash

Two drugs are better than one for ovarian cancer (Karen Ring). Earlier this week, scientists from UCLA reported that a combination drug therapy could be an effective treatment for 50% of aggressive ovarian cancers. The study was published in the journal Precision Oncology and was led by Dr. Sanaz Memarzadeh.

Women with high-grade ovarian tumors have an 85% chance of tumor recurrence after treatment with a common chemotherapy drug called carboplatin. The UCLA team found in a previous study that ovarian cancer stem cells are to blame because they are resistant to carboplatin. It’s because these stem cells have an abundance of proteins called cIAPs, which prevent cell death from chemotherapy.

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Ovarian cancer cells (blue) expressing cIAP protein (red) on the left are more sensitive to a combination therapy than cancer cells that don’t express the protein on the right. (UCLA Broad Stem Cell Research Center/Precision Oncology)

Memarzadeh discovered that an experimental drug called birinapant made some ovarian cancer tumors more sensitive to chemotherapy treatment by breaking down cIAPs. This gave her the idea that combining the two drugs, birinapant and carboplatin, might be a more effective strategy for treating aggressive ovarian tumors.

By treating with the two drugs simultaneously, the scientists improved the survival rate of mice with ovarian cancer. They also tested this combo drug treatment on 23 ovarian cancer cell lines derived from women with highly aggressive tumors. The treatment killed off half of the cell lines indicating that some forms of this cancer are resistant to the combination treatment.

When they measured the levels of cIAPs in the human ovarian cancer cell lines, they found that high levels of the proteins were associated with ovarian tumor cells that responded well to the combination treatment. This is exciting because it means that clinicians can analyze tumor biopsies for cIAP levels to determine whether certain ovarian tumors would respond well to combination therapy.

Memarzadeh shared her plans for future research in a UCLA news release,

“I believe that our research potentially points to a new treatment option. In the near future, I hope to initiate a phase 1/2 clinical trial for women with ovarian cancer tumors predicted to benefit from this combination therapy.”

In a first, researchers create inner ear tissue. From heart muscle to brain cells to insulin-producing cells, researchers have figured out how to make a long list of different human cell types using induced pluripotent stem cells (iPSCs) – cells taken from the body and reprogrammed into a stem cell-like state.

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Human inner ear organoid with sensory hair cells (cyan) and sensory neurons (yellow). An antibody for the protein CTBP2 reveals cell nuclei as well as synapses between hair cells and neurons (magenta). | Photo: Karl Koehler

This week, a research group at the Indiana University School of Medicine successfully added inner ear cells to that list. This feat, published in Nature Biotechnology, is especially important given the fact that the inner ear is one of the few parts of the body that cannot be biopsied for further examination. With these cells in hands, new insights into the causes of hearing loss and balance disorders may be on the horizon.

The inner ear contains 75,000 sensory hair cells that convert sound waves into electrical signals to the brain. Loud noises, drug toxicity, and genetic mutations can permanently damage the hair cells leading to hearing loss and dizziness. Over 15%  of the U.S. population have some form of hearing loss and that number swells to 67% for people over 75.

Due to the complex shape of the inner ear, the team grew the iPSCs into three dimensional balls of cells rather than growing them as a flat layer of cells on a petri dish. With educated guesses sprinkled in with some trial and error, the scientists, for the time, identified a recipe of proteins that stimulated the iPSCs to transform into inner ear tissue. And like any great recipe, it wasn’t so much the ingredient list but the timing that was key:

“If you apply these signals at the wrong time you can potentially generate a brain instead of an inner ear,” first author Dr. Karl Koehler said in an interview with Gizmodo. “The real breakthrough is that we figured out the exact timing to do each one of these [protein] treatments.”

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Senior author, Eri Hashino, Ph.D., and first author, Karl R. Koehler, Ph.D. Photo: Indiana University

Careful examination shows that the tissue, referred to as organoids, not only contained the sensory hair cells of the inner ear cell but also nerve cells, or neurons, that are responsible for relaying the sound waves to the brain. Koehler explained the importance of this result in a press release:

“We also found neurons, like those that transmit signals from the ear to the brain, forming connections with sensory cells. This is an exciting feature of these organoids because both cell types are critical for proper hearing and balance.”

Though it’s still early days, these iPSC-derived inner ear organoids are a key step toward the ultimate goal of repairing hearing loss. Senior author, Dr. Eri Hashino, talked about the team’s approach to reach that goal:

“Up until now, potential drugs or therapies have been tested on animal cells, which often behave differently from human cells. We hope to discover new drugs capable of helping regenerate the sound-sending hair cells in the inner ear of those who have severe hearing problems.”

This man’s research is no fish tale
And finally, we leave you this week with a cool article and video by STAT. It features Dr. Leonard Zon of Harvard University and his many, many tanks full of zebrafish. This little fish has made a huge splash in understanding human development and disease. But don’t take my word for it, watch the video!

Stem cell stories that caught our eye: developing the nervous system, aging stem cells and identical twins not so identical

Here are the stem cell stories that caught our eye this week. Enjoy!

New theory for how the nervous system develops.

There’s a new theory on the block for how the nervous system is formed thanks to a study published yesterday by UCLA stem cell scientists in the journal Neuron.

The theory centers around axons, thin extensions projecting from nerve cells that transmit electrical signals to other cells in the body. In the developing nervous system, nerve cells extend axons into the brain and spinal cord and into our muscles (a process called innervation). Axons are guided to their final destinations by different chemicals that tell axons when to grow, when to not grow, and where to go.

Previously, scientists believed that one of these important chemical signals, a protein called netrin 1, exerted its influence over long distances in a gradient-like fashion from a structure in the developing nervous system called the floor plate. You can think of it like a like a cell phone tower where the signal is strongest the closer you are to the tower but you can still get some signal even when you’re miles away.

The UCLA team, led by senior author and UCLA professor Dr. Samantha Butler, questioned this theory because they knew that neural progenitor cells, which are the precursors to nerve cells, produce netrin1 in the developing spinal cord. They believed that the netrin1 secreted from these progenitor cells also played a role in guiding axon growth in a localized manner.

To test their hypothesis, they studied neural progenitor cells in the developing spines of mouse embryos. When they eliminated netrin1 from the neural progenitor cells, the axons went haywire and there was no rhyme or reason to their growth patterns.

Left: axons (green, pink, blue) form organized patterns in the normal developing mouse spinal cord. Right: removing netrin1 results in highly disorganized axon growth. (UCLA Broad Stem Cell Research Center/Neuron)

A UCLA press release explained what the scientists discovered next,

“They found that neural progenitors organize axon growth by producing a pathway of netrin1 that directs axons only in their local environment and not over long distances. This pathway of netrin1 acts as a sticky surface that encourages axon growth in the directions that form a normal, functioning nervous system.”

Like how ants leave chemical trails for other ants in their colony to follow, neural progenitor cells leave trails of netrin1 in the spinal cord to direct where axons go. The UCLA team believes they can leverage this newfound knowledge about netrin1 to make more effective treatments for patients with nerve damage or severed nerves.

In future studies, the team will tease apart the finer details of how netrin1 impacts axon growth and how it can be potentially translated into the clinic as a new therapeutic for patients. And from the sounds of it, they already have an idea in mind:

“One promising approach is to implant artificial nerve channels into a person with a nerve injury to give regenerating axons a conduit to grow through. Coating such nerve channels with netrin1 could further encourage axon regrowth.”

Age could be written in our stem cells.

The Harvard Gazette is running an interesting series on how Harvard scientists are tackling issues of aging with research. This week, their story focused on stem cells and how they’re partly to blame for aging in humans.

Stem cells are well known for their regenerative properties. Adult stem cells can rejuvenate tissues and organs as we age and in response to damage or injury. However, like most house hold appliances, adult stem cells lose their regenerative abilities or effectiveness over time.

Dr. David Scadden, co-director of the Harvard Stem Cell Institute, explained,

“We do think that stem cells are a key player in at least some of the manifestations of age. The hypothesis is that stem cell function deteriorates with age, driving events we know occur with aging, like our limited ability to fully repair or regenerate healthy tissue following injury.”

Harvard scientists have evidence suggesting that certain tissues, such as nerve cells in the brain, age sooner than others, and they trigger other tissues to start the aging process in a domino-like effect. Instead of treating each tissue individually, the scientists believe that targeting these early-onset tissues and the stem cells within them is a better anti-aging strategy.

David Sadden, co-director of the Harvard Stem Cell Institute.
(Jon Chase/Harvard Staff Photographer)

Dr. Scadden is particularly interested in studying adult stem cell populations in aging tissues and has found that “instead of armies of similarly plastic stem cells, it appears there is diversity within populations, with different stem cells having different capabilities.”

If you lose the stem cell that’s the best at regenerating, that tissue might age more rapidly.  Dr. Scadden compares it to a game of chess, “If we’re graced and happen to have a queen and couple of bishops, we’re doing OK. But if we are left with pawns, we may lose resilience as we age.”

The Harvard Gazette piece also touches on a changing mindset around the potential of stem cells. When stem cell research took off two decades ago, scientists believed stem cells would grow replacement organs. But those days are still far off. In the immediate future, the potential of stem cells seems to be in disease modeling and drug screening.

“Much of stem cell medicine is ultimately going to be ‘medicine,’” Scadden said. “Even here, we thought stem cells would provide mostly replacement parts.  I think that’s clearly changed very dramatically. Now we think of them as contributing to our ability to make disease models for drug discovery.”

I encourage you to read the full feature as I only mentioned a few of the highlights. It’s a nice overview of the current state of aging research and how stem cells play an important role in understanding the biology of aging and in developing treatments for diseases of aging.

Identical twins not so identical (Todd Dubnicoff)

Ever since Takahashi and Yamanaka showed that adult cells could be reprogrammed into an embryonic stem cell-like state, researchers have been wrestling with a key question: exactly how alike are these induced pluripotent stem cells (iPSCs) to embryonic stem cells (ESCs)?

It’s an important question to settle because iPSCs have several advantages over ESCs. Unlike ESCs, iPSCs don’t require the destruction of an embryo so they’re mostly free from ethical concerns. And because they can be derived from a patient’s cells, if iPSC-derived cell therapies were given back to the same patient, they should be less likely to cause immune rejection. Despite these advantages, the fact that iPSCs are artificially generated by the forced activation of specific genes create lingering concerns that for treatments in humans, delivering iPSC-derived therapies may not be as safe as their ESC counterparts.

Careful comparisons of DNA between iPSCs and ESCs have shown that they are indeed differences in chemical tags found on specific spots on the cell’s DNA. These tags, called epigenetic (“epi”, meaning “in addition”) modifications can affect the activity of genes independent of the underlying genetic sequence. These variations in epigenetic tags also show up when you compare two different preparations, or cell lines, of iPSCs. So, it’s been difficult for researchers to tease out the source of these differences. Are these differences due to the small variations in DNA sequence that are naturally seen from one cell line to the other? Or is there some non-genetic reason for the differences in the iPSCs’ epigenetic modifications?

Marian and Vivian Brown, were San Francisco’s most famous identical twins. Photo: Christopher Michel

A recent CIRM-funded study by a Salk Institute team took a clever approach to tackle this question. They compared epigenetic modifications between iPSCs derived from three sets of identical twins. They still found several epigenetic variations between each set of twins. And since the twins have identical DNA sequences, the researchers could conclude that not all differences seen between iPSC cell lines are due to genetics. Athanasia Panopoulos, a co-first author on the Cell Stem Cell article, summed up the results in a press release:

“In the past, researchers had found lots of sites with variations in methylation status [specific term for the epigenetic tag], but it was hard to figure out which of those sites had variation due to genetics. Here, we could focus more specifically on the sites we know have nothing to do with genetics. The twins enabled us to ask questions we couldn’t ask before. You’re able to see what happens when you reprogram cells with identical genomes but divergent epigenomes, and figure out what is happening because of genetics, and what is happening due to other mechanisms.”

With these new insights in hand, the researchers will have a better handle on interpreting differences between individual iPSC cell lines as well as their differences with ESC cell lines. This knowledge will be important for understanding how these variations may affect the development of future iPSC-based cell therapies.

Stem Cell Stories That Caught our Eye: Making blood and muscle from stem cells and helping students realize their “pluripotential”

Stem cells offer new drug for blood diseases. A new treatment for blood disorders might be in the works thanks to a stem cell-based study out of Harvard Medical School and Boston Children’s hospital. Their study was published in the journal Science Translational Medicine.

The teams made induced pluripotent stem cells (iPSCs) from the skin of patients with a rare blood disorder called Diamond-Blackfan anemia (DBA) – a bone marrow disease that prevents new blood cells from forming. iPSCs from DBA patients were then specialized into blood progenitor cells, the precursors to blood cells. However, these precursor cells were incapable of forming red blood cells in a dish like normal precursors do.

Red blood cells were successfully made via induced pluripotent stem cells from a Diamond-Blackfan anemia patient. Image: Daley lab, Boston Children’s

Red blood cells were successfully made via induced pluripotent stem cells from a Diamond-Blackfan anemia patient. Image: Daley lab, Boston Children’s

The blood progenitor cells from DBA patients were then used to screen a library of compounds to identify drugs that could get the DBA progenitor cells to develop into red blood cells. They found a compound called SMER28 that had this very effect on progenitor cells in a dish. When the compound was tested in zebrafish and mouse models of DBA, the researchers observed an increase in red blood cell production and a reduction of anemia symptoms.

Getting pluripotent stem cells like iPSCs to turn into blood progenitor cells and expand these cells into a population large enough for drug screening has not been an easy task for stem cell researchers.

Co-first author on the study, Sergei Doulatov, explained in a press release, “iPS cells have been hard to instruct when it comes to making blood. This is the first time iPS cells have been used to identify a drug to treat a blood disorder.”

In the future, the researchers will pursue the questions of why and how SMER28 boosts red blood cell generation. Further work will be done to determine whether this drug will be a useful treatment for DBA patients and other blood disorders.

 

Students realize their “pluripotential”. In last week’s stem cell stories, I gave a preview about an exciting stem cell “Day of Discovery” hosted by USC Stem Cell in southern California. The event happened this past Saturday. Over 500 local middle and high school students attended the event and participated in lab tours, poster sessions, and a career resource fair. Throughout the day, they were engaged by scientists and educators about stem cell science through interactive games, including the stem cell edition of Family Feud and a stem cell smartphone videogame developed by USC graduate students.

In a USC press release, Rohit Varma, dean of the Keck School of Medicine of USC, emphasized the importance of exposing young students to research and scientific careers.

“It was a true joy to welcome the middle and high school students from our neighboring communities in Boyle Heights, El Sereno, Lincoln Heights, the San Gabriel Valley and throughout Los Angeles. This bright young generation brings tremendous potential to their future pursuits in biotechnology and beyond.”

Maria Elena Kennedy, a consultant to the Bassett Unified School District, added, “The exposure to the Keck School of Medicine of USC is invaluable for the students. Our students come from a Title I School District, and they don’t often have the opportunity to come to a campus like the Keck School of Medicine.”

The day was a huge success with students posting photos of their experiences on social media and enthusiastically writing messages like “stem cells are our future” and “USC is my goal”. One high school student acknowledged the opportunity that this day offers to students, “California currently has biotechnology as the biggest growing sector. Right now, it’s really important that students are visiting labs and learning more about the industry, so they can potentially see where they’re going with their lives and careers.”

You can read more about USC’s Stem Cell Day of Discovery here. Below are a few pictures from the event courtesy of David Sprague and USC.

Students have fun with robots representing osteoblast and osteoclast cells at the Stem Cell Day of Discovery event held at the USC Health Sciences Campus in Los Angeles, CA. February 4th, 2017. The event encourages students to learn more about STEM opportunities, including stem cell study and biotech, and helps demystify the fields and encourage student engagement. Photo by David Sprague

Students have fun with robots representing osteoblast and osteoclast cells at the USC Stem Cell Day of Discovery. Photo by David Sprague

Dr. Francesca Mariana shows off a mouse skeleton that has been dyed to show bones and cartilage at the Stem Cell Day of Discovery event held at the USC Health Sciences Campus in Los Angeles, CA. February 4th, 2017. The event encourages students to learn more about STEM opportunities, including stem cell study and biotech, and helps demystify the fields and encourage student engagement. Photo by David Sprague

Dr. Francesca Mariana shows off a mouse skeleton that has been dyed to show bones and cartilage. Photo by David Sprague

USC masters student Shantae Thornton shows students how cells are held in long term cold storage tanks at -195 celsius at the Stem Cell Day of Discovery event held at the USC Health Sciences Campus in Los Angeles, CA. February 4th, 2017. The event encourages students to learn more about STEM opportunities, including stem cell study and biotech, and helps demystify the fields and encourage student engagement. Photo by David Sprague

USC masters student Shantae Thornton shows students how cells are held in long term cold storage tanks at -195 celsius. Photo by David Sprague

Genesis Archila, left, and Jasmine Archila get their picture taken at the Stem Cell Day of Discovery event held at the USC Health Sciences Campus in Los Angeles, CA. February 4th, 2017. The event encourages students to learn more about STEM opportunities, including stem cell study and biotech, and helps demystify the fields and encourage student engagement. Photo by David Sprague

Genesis Archila, left, and Jasmine Archila get their picture taken at the USC Stem Cell Day of Discovery. Photo by David Sprague

New stem cell recipes for making muscle: new inroads to study muscular dystrophy (Todd Dubnicoff)

Embryonic stem cells are amazing because scientists can change or specialize them into virtually any cell type. But it’s a lot easier said than done. Researchers essentially need to mimic the process of embryo development in a petri dish by adding the right combination of factors to the stem cells in just the right order at just the right time to obtain a desired type of cell.

Making human muscle tissue from embryonic stem cells has proven to be a challenge. The development of muscle, as well as cartilage and bone, are well characterized and known to form from an embryonic structure called a somite. Researches have even been successful working out the conditions for making somites from animal stem cells. But those recipes didn’t work well with human stem cells.

Now, a team of researchers at the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA has overcome this roadblock by carrying out a systematic approach using human tissue. As described in Cell Reports, the scientists isolated somites from early human embryos and studied their gene activity. By comparing somites that were just beginning to emerge with fully formed somites, the researchers pinpointed differences in gene activity patterns. With this data in hand, the team added factors to the cells that were known to affect the activity of those genes. Through some trial and error, they produced a recipe – different than those used in animal cells – that could convert 90 percent of the human stem cells into somites in only four days. Those somites could then readily transform into muscle or bone or cartilage.

This new method for making human muscle will be critical for the lab’s goal to develop therapies for Duchenne muscular dystrophy, an incurable muscle wasting disease that strikes young boys and is usually fatal by their 20’s.

The new protocol turned 90 percent of human pluripotent stem cells into somite cells in just four days; those somite cells then generated (left to right) cartilage, bone and muscle cells.  Image: April Pyle Lab/UCLA

The new protocol turned 90 percent of human pluripotent stem cells into somite cells in just four days; those somite cells then generated (left to right) cartilage, bone and muscle cells. Image: April Pyle Lab/UCLA