Stem cell stories that caught our eye: turning on T cells; fixing our brains; progress and trends in stem cells; and one young man’s journey to recover from a devastating injury

Healthy_Human_T_Cell

A healthy T cell

Here are some stem cell stories that caught our eye this past week. Some are groundbreaking science, others are of personal interest to us, and still others are just fun.

Directing the creation of T cells. To paraphrase the GOP Presidential nominee, any sane person LOVES, LOVES LOVES their T cells, in a HUGE way, so HUGE. They scamper around the body getting rid of viruses and the tiny cancers we all have in us all the time. A CIRM-funded team at CalTech has worked out the steps our genetic machinery must take to make more of them, a first step in letting physicians turn up the action of our immune systems.

We have known for some time the identity of the genetic switch that is the last, critical step in turning blood stem cells into T cells, but nothing in our body is as simple as a single on-off event. The Caltech team isolated four genetic factors in the path leading to that main switch and, somewhat unsuspected, they found out those four steps had to be activated sequentially, not all at the same time. They discovered the path by engineering mouse cells so that the main T cell switch, Bcl11b, glows under a microscope when it is turned on.

“We identify the contributions of four regulators of Bcl11b, which are all needed for its activation but carry out surprisingly different functions in enabling the gene to be turned on,” said Ellen Rothenberg, the senior author in a university press release picked up by Innovations Report. “It’s interesting–the gene still needs the full quorum of transcription factors, but we now find that it also needs them to work in the right order.”

Video primer on stem cells in the brain.  In conjunction with an article in its August issue, Scientific American posted a video from the Brain Forum in Switzerland of Elena Cattaneo of the University of Milan explaining the basics of adult versus pluripotent stem cells, and in particular how we are thinking about using them to repair diseases in the brain.

The 20-minute talk gives a brief review of pioneers who “stood alone in unmarked territory.” She asks how can stem cells be so powerful; and answers by saying they have lots of secrets and those secrets are what stem cell scientist like her are working to unravel.  She notes stem cells have never seen a brain, but if you show them a few factors they can become specialized nerves. After discussing collaborations in Europe to grow replacement dopamine neurons for Parkinson’s disease, she went on to describe her own effort to do the same thing in Huntington’s disease, but in this case create the striatal nerves lost in that disease.

The video closes with a discussion of how basic stem cell research can answer evolutionary questions, in particular how genetic changes allowed higher organisms to develop more complex nervous systems.

kelley and kent

CIRM Science Officers Kelly Shepard and Kent Fitzgerald

A stem cell review that hits close to home.  IEEE Pulse, a publication for scientists who mix engineering and medicine and biology, had one of their reporters interview two of our colleagues on CIRM’s science team. They asked senior science officers Kelly Shepard and Kent Fitzgerald to reflect on how the stem cell field has progressed based on their experience working to attract top researchers to apply for our grants and watching our panel of outside reviewers select the top 20 to 30 percent of each set of applicants.

One of the biggest changes has been a move from animal stem cell models to work with human stem cells, and because of CIRM’s dedicated and sustained funding through the voter initiative Proposition 71, California scientists have led the way in this change. Kelly described examples of how mouse and human systems are different and having data on human cells has been critical to moving toward therapies.

Kelly and Kent address several technology trends. They note how quickly stem cell scientists have wrapped their arms around the new trendy gene editing technology CRISPR and discuss ways it is being used in the field. They also discuss the important role of our recently developed ability to perform single cell analysis and other technologies like using vessels called exosomes that carry some of the same factors as stem cells without having to go through all the issues around transplanting whole cells.

“We’re really looking to move things from discovery to the clinic. CIRM has laid the foundation by establishing a good understanding of mechanistic biology and how stem cells work and is now taking the knowledge and applying it for the benefit of patients,” Kent said toward the end of the interview.

jake and family

Jake Javier and his family

Jake’s story: one young man’s journey to and through a stem cell transplant; As a former TV writer and producer I tend to be quite critical about the way TV news typically covers medical stories. But a recent story on KTVU, the Fox News affiliate here in the San Francisco Bay Area, showed how these stories can be done in a way that balances hope, and accuracy.

Reporter Julie Haener followed the story of Jake Javier – we have blogged about Jake before – a young man who broke his spine and was then given a stem cell transplant as part of the Asterias Biotherapeutics clinical trial that CIRM is funding.

It’s a touching story that highlights the difficulty treating these injuries, but also the hope that stem cell therapies holds out for people like Jake, and of course for his family too.

If you want to see how a TV story can be done well, this is a great example.

Adding new stem cell tools to the Parkinson’s disease toolbox

Understanding a complicated neurodegenerative disorder like Parkinson’s disease (PD) is no easy task. While there are known genetic risk factors that cause PD, only about 10 percent of cases are linked to a genetic cause. The majority of patients suffer from the sporadic form of PD, where the causes are unknown but thought to be a combination of environmental, lifestyle and genetic factors.

Unfortunately, there is no cure for PD, and current treatments only help PD patients manage the symptoms of their disease and inevitably lose their effectiveness over time. Another troubling issue is that doctors and scientists don’t have good ways to predict who is at risk for PD, which closes an important window of opportunity for delaying the onset of this devastating disease.

Scientists have long sought relevant disease models that mimic the complicated pathological processes that occur in PD. Current animal models have failed to truly represent what is going on in PD patients. But the field of Parkinson’s research is not giving up, and scientists continue to develop new and improved tools, many of them based on human stem cells, to study how and why this disease happens.

New Stem Cell Tools for Parkinson’s

Speaking of new tools, scientists from the Buck Institute for Research on Aging published a study that generated 10 induced pluripotent stem cell (iPS cell) lines derived from PD patients carrying well known genetic mutations linked to PD. These patient cell lines will be a useful resource for studying the underlying causes of PD and for potentially identifying therapeutics that prevent or treat this disorder. The study was partly funded by CIRM and was published today in the journal PLOS ONE.

Dr. Xianmin Zeng, the senior author on the study and Associate Professor at Buck Institute, developed these disease cell lines as tools for the larger research community to use. She explained in a news release:

Xianmin Zeng, Buck Institute

Xianmin Zeng, Buck Institute

“We think this is the largest collection of patient-derived lines generated at an academic institute. We believe the [iPS cell] lines and the datasets we have generated from them will be a valuable resource for use in modeling PD and for the development of new therapeutics.”

 

The datasets she mentions are part of a large genomic analysis that was conducted on the 10 patient stem cell lines carrying common PD mutations in the SNCA, PARK2, LRRK2, or GBA genes as well as control stem cell lines derived from healthy patients of the same age. Their goal was to identify changes in gene expression in the Parkinson’s stem cell lines as they matured into the disease-affected nerve cells of the brain that could yield clues into how PD develops at the molecular level.

Using previous methods developed in her lab, Dr. Zeng coaxed the iPS cell lines into neural stem cells (brain stem cells) and then further into dopaminergic neurons – the nerve cells that are specifically affected and die off in Parkinson’s patients. Eight of the ten patient lines were able to generate neural stem cells, and all of the neural stem cell lines could be coaxed into dopaminergic neurons – however, some lines were better at making dopaminergic neurons than others.

Dopaminergic neurons derived from induced pluripotent stem cells. (Xianmin Zeng, Buck Institute)

Dopaminergic neurons derived from induced pluripotent stem cells. (Xianmin Zeng, Buck Institute)

When they analyzed these lines, surprisingly they found that the overall gene expression patterns were similar between diseased and healthy cell lines no matter what cell stage they were at (iPS cells, neural stem cells, and neurons). They next stressed the cells by treating them with a drug called MPTP that is known to cause Parkinson’s like symptoms in humans. MPTP treatment of dopaminergic neurons derived from PD patient iPS cell lines did cause changes in gene expression specifically related to mitochondrial function and death, but these changes were also seen in the healthy dopaminergic neurons.

Parkinson’s, It’s complicated…

These interesting findings led the authors to conclude that while their new stem cell tools certainly display some features of PD, individually they are not sufficient to truly model all aspects of PD because they represent a monogenic (caused by a single mutation) form of the disease.

They explain in their conclusion that the power of their PD patient iPS cell lines will be achieved when combined with additional patient lines, better controls, and more focused data analysis:

“Our studies suggest that using single iPSC lines for drug screens in a monogenic disorder with a well-characterized phenotype may not be sufficient to determine causality and mechanism of action due to the inherent variability of biological systems. Developing a database to increase the number of [iPS cell] lines, stressing the system, using isogenic controls [meaning the lines have identical genes], and using more focused strategies for analyzing large scale data sets would reduce the impact of line-to-line variations and may provide important clues to the etiology of PD.”

Brian Kennedy, Buck Institute President and CEO, also pointed out the larger implications of this study by commenting on how these stem cell tools could be used to identify potential drugs that specifically target certain Parkinson’s mutations:

Brian Kennedy, Buck Institute

Brian Kennedy, Buck Institute

“This work combined with dozens of other control, isogenic and reporter iPSC lines developed by Dr. Zeng will enable researchers to model PD in a dish. Her work, which we are extremely proud of, will help researchers dissect how genes interact with each other to cause PD, and assist scientists to better understand what experimental drugs are doing at the molecular level to decide what drugs to use based on mutations.”

Overall, what inspires me about this study is the author’s mission to provide a substantial number of PD patient stem cell lines and genomic analysis data to the research community. Hopefully their efforts will inspire other scientists to add more stem cell tools to the Parkinson’s tool box. As the saying goes, “it takes an army to move a mountain”, in the case of curing PD, the mountain seems more like Everest, and we need all the tools we can get.


Related links:

You Call It Corn Stem Cells, We Call It An A-Maize-Ing Hope to Feed the World

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David Jackson and his team at Cold Spring Harbor Laboratory identify a unique genetic pathway that regulated stem cell growth. Certain mutations in the pathway lead to increased plant yields (two plants on the right). Image: Cold Spring Harbor Laboratory

Here at the Stem Cellar, we’re laser-beam focused on the exciting progress being made to bring stem cell-based treatments to patients with unmet medical needs. But what good will those life-saving treatments be if the patients end up starving from hunger? It’s a serious question to ask considering the world’s diminishing farmlands and yet another record-breaking month for global warming in the books.

Based on a study published yesterday by Cold Spring Harbor Laboratory researchers, our friend the stem cell emerges again as a source of hope. Reporting in Nature Genetics, the team uncovered an important genetic switch in the stem cells of corn that when manipulated can lead to a 50% increase in the size of the corn.

Plants have stem cells too
Plants do indeed have stem cells that reside in an area called the meristem and function similarly to their animal counterparts. The root apical meristem is responsible for providing cells for root growth while the shoot apical meristem gives rise to plant organs like leaves and flowers. Previous research had shown that a signal system within the meristem communicates whether or not to turn on stem cell growth. The current study identified protein signals involved in a similar regulatory circuit but with an intriguing difference which David Jackson, the lead author on the study, explained in a Cold Spring Harbor video (see below):

“In this new study we found that actually the leaves, the developing leaves, send a signal back to the stem cells to control their growth which is really a new finding.”

FCP-1/FEA3: A Leaf to Stem Cell Braking System
The proteins involved in this signal include a receptor protein on the stem cells called FEA3 and a protein from the leaves called FCP-1. When it travels from the leaves to the stem cells, FCP-1 binds to FEA3 causing an inhibition of stem cell growth. So you’d think that disrupting this pathway would release the “brake” on stem cell growth and lead to tractor-sized corn. But when the team tested that idea by growing plants with a fea3 mutation, the resulting crop was short and stubby. The explanation is that too many stem cells is not a good thing and the available water, sunlight, and soil is not enough to support increased growth.

Easing off the brakes is better for crop yields
So as a result of uncontrolled stem cell growth, the corn becomes deformed and leads to a poorer yield. But next, the team analyzed plants with weaker versions, or alleles, of the fea3 mutations. Basically, these mutations still lead to a release of the “brake” on stem cell growth but not as quite as much as the initial fea3 mutation. Under this genetic scenario, the plants grew extra rows of kernels with up to 50% increase in yield.

Because the FCP-1/FEA3 pathway is found throughout the plant kingdom, this result has the tantalizing potential to help increase yields of all sorts of food crops.  As Jackson mentions in an interview with Gizmodo, this future will depend on these laboratory experiments working in a real world setting:

“If the yield increases we have seen in our lab strains hold out when used in agricultural maize strains this would lead to a significant boost in yields, potentially improving agricultural sustainability by requiring less land be devoted to agriculture. The same approaches could also benefit farmers in developing countries growing a wide range of crops.”

Certainly this future crop would be considered a genetically modified organism (GMO) which may concern some. But just today the National Academies of Sciences, Engineering, and Medicine posted evidence on their website that points to GMO foods as being safe and good for the environment.

Brave new world or dark threatening future: a clear-eyed look at genome editing and what it means for humanity

Frankenstein

   Is this the face of the future?

“Have you ever wished that there were something different about yourself? Maybe you imagined yourself taller, thinner or stronger? Smarter? More attractive? Healthier?”

That’s the question posed by UC Davis stem cell researcher (and CIRM grantee) Paul Knoepfler at the start of his intriguing new book ‘GMO Sapiens: The Life-Changing Science of Designer Babies’.

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You can find GMO Sapiens on Amazon.com

The book is a fascinating, and highly readable, and takes a unique look at the dramatic advances in technology that allow us to edit the human genome in ways that could allow us to do more than just create “designer babies”, it could ultimately help us change the definition of what it means to be human.

Paul begins by looking at the temptation to use technologies like CRISPR (we have blogged about this here), to genetically edit or alter human embryos so that the resulting child is enhanced in some ways. It could be that the editing is used to remove a genetic mutation that could cause a deadly disease (such as the BRCA1 gene that puts women at increased risk of breast and ovarian cancer) or it could be that the technique is used to give a baby blue eyes, to make it taller, more athletic, or to simply eliminate male pattern baldness later in life.

Paul says those latter examples are not as ridiculous as they sound:

Paul Knoepfler

Paul Knoepfler

“If you think these ideas sound far-fetched, consider that Americans alone spend tens of billions of dollars each year on plastic surgery procedures and creams to try to achieve these kinds of goals. Some of the time elective cosmetic surgery is done on children. In the future, we might have “cosmetic genetic surgeons” who do “surgery” on our family’s genes for cosmetic reasons. In other countries the sensibilities and cultural expectations could lead to other kinds of genetic modifications of humans for “enhancements”.

While the technology that enables us to do this is new, the ideas behind why we would want to do this are far from new. Paul delves into those ideas including a look at the growth of the eugenics movement in the late 19th and early 20th century advocating the improvement of human genetic traits through higher reproductive rates for people considered “superior”. And there was a darker side to the movement:

“Indiana had instituted the first law for sterilization of “inferior” people in the world in 1907. Astonishingly this state law and then similar laws (the original was revoked, but a new law was passed later) stayed on the books in that state until 1974.

This led to approximately 2,500 governmentally forced sterilizations. The poor, uneducated, people of color, Native Americans, and people with disabilities were disproportionately targeted.”

Paul explores the ethical and moral implications of changing our genetic code, changes that can then be passed on to future generations. While he understands the desire to use these technologies to create positive changes, he is also very clear in his concerns that we don’t yet have enough knowledge to be able to use them in a safe manner.

“CRISPR can literally re-write the genomic book inside of us. However, it remains unknown how often it might go to the wrong page or paragraph, so to speak, or stay on the right page, but make an undesired edit there.”

Tiny errors in editing the genome, particularly at such an early stage in an embryo’s development, could have profound and unintended consequences years down the road, resulting in physical or developmental problems we can’t anticipate or predict. For example, you might remove the susceptibility to one disease only to create an even larger problem, one that is now embedded in that person’s DNA and ready to be passed on to subsequent generations.

The book includes interviews with key figures in the field – scientists, bioethicists etc. – and covers a wide range of views of what we should do. For example, the Director of the US National Institutes of Health (NIH), Francis Collins, said that designer babies “make good Hollywood — and bad science,” while the Center for Genetics and Society has advocated for a moratorium on human genetic modification in the US.

In contrast, scientists such as Harvard professor George Church and CRISPR pioneer Jennifer Doudna of UC Berkeley, say we need to carefully explore how to harness the potential for these technologies.

For Church it is a matter of choice:

“The new technology enables parents to make choices about their children just as they might with Ritalin or cleft palate surgery to ‘improve’ behavior or appearance.”

For Doudna it’s acknowledging the fact that you can’t put the genie back in the bottle:

“There’s no way to unlearn what is learned. We can’t put this technology to bed. If a person has basic knowledge of molecular biology they can do it. It’s not realistic to think we can block it…We want to put out there the information that people would need to make an informed decision, to encourage appropriate research and discourage forging ahead with clinical applications that could be dangerous or raise ethical issues.”

The power of Paul’s book is that while it does not offer any easy answers, it does raise many important questions.

It’s a wonderfully well-written book that anyone can read, even someone like me who doesn’t have a science background. He does a good job of leading the reader through the development of these technologies (from the basic idea of genetically altering plants to make them disease resistant) to the portrayal of these concepts in literature (Frankenstein and Brave New World) to movies (Gattaca – 4 stars on Rotten Tomatoes  a great film if you haven’t already seen it).

It’s clear where Paul stands on the issue; he believes there should be a moratorium on human genetic modification until we have a much deeper understanding of the science behind it, and the ethics and morality underpinning it:

“This is a very exciting time to be alive and we should be open to embracing change, but not blindly or in a rush. Armed with information and passion, we can have a major, positive impact on how this biotech revolution unfolds and impacts humanity.”

By the way, Paul also has one of the most widely read blogs about stem cells, where you can read more about his thoughts on CRISPR and other topics.

 

CIRM-funded study suggests methods to make pluripotent stem cells are safe

We live in an era where stem cell treatments are already being tested in human clinical trials for eye disease, spinal cord injury, and type 1 diabetes. The hope is that transplanting stem cells or their cell derivatives will replace diseased tissue, restore function, and cure patients – all while being safe and without causing negative side effects.

Safety will be the key to the future success of stem cell replacement therapies. We’ve learned our lesson from early failed gene therapy experiments where genetically altered stem cells that were supposed to help patients actually caused them to get cancer. Science has since developed methods of gene therapy that appear safe, but new concerns have cropped up around the safety of the methods used to generate pluripotent stem cells, which are considered a potential starting material for cell replacement therapies.

Stem cell reprogramming can cause problems

Induced pluripotent stem cells (iPS cells) cultured in a dish.

Induced pluripotent stem cells (iPS cells) cultured in a dish.

Induced pluripotent stem cells, or iPS cells, are a potential source of pluripotent stem cells for cell therapy. These cells are equivalent to embryonic stem cells but can be generated from adult tissue (such as skin or even blood) by reprogramming cells back to a pluripotent state. During cellular reprogramming, one set of genes is turned off and another set is turned on through a process called epigenetic remodeling. We don’t have time to explain epigenetics in this blog, but to be brief, it involves chromatin remodeling (chromatin is the complex of DNA and protein that make up chromosomes) and is essential for controlling gene expression.

To make healthy iPS cells, the intricate steps involved in cellular reprogramming and epigenetic remodeling have to be coordinated perfectly. Scientists worry that these processes aren’t always perfect and that cancer-causing mutations could be introduced that could cause tumors when transplanted into patients.

A CIRM-funded study published Friday in Nature Communications offers some relief to this potential roadblock to using reprogrammed iPS cells for cell therapy. Scientists from The Scripps Research Institute (TSRI) and the J. Craig Venter Institute (JCVI) collaborated on a study that assessed the safety of three common methods for generating iPS cells. Their findings suggest that these reprogramming methods are relatively safe and unlikely to give cancer-causing mutations to patients.

Comparing three reprogramming methods

In case you didn’t know, iPS cells are typically made by turning on expression of four genes – OCT4, SOX2, KLF4, and c-MYC – that maintain stem cells in a pluripotent state. Scientists can force an adult cell to express these genes by delivering extra copies into the cell. In this study, the scientists conducted a comparative genomic analysis of three commonly used iPS cell reprogramming methods (integrating retroviral vectors, non-integrating Sendai virus, and synthetic mRNAs) to search for potential cancer-causing mutations in the DNA of the iPS cells.

Unlike previous studies that focused on finding a single type of genetic mutation in reprogrammed iPS cells, the group looked at multiple types of genetic mutations – from single nucleotide changes in DNA to large structural variations – by comparing whole-genome sequencing data of the starting parental cells (skin cells) to iPS cells.

They concluded that the three reprogramming methods generally do not cause serious problems and hypothesized that cancer-causing mutations likely happen at a later step after the iPS cells are already made, an issue the team is addressing in ongoing work.

They explained in their publication:

“We detected subtle differences in the numbers of [genetic] variants depending on the method, but rarely found mutations in genes that have any known association with increased cancer risk. We conclude that mutations that have been reported in iPS cell cultures are unlikely to be caused by their reprogramming, but instead are probably due to the well-known selective pressures that occur when hPSCs [human pluripotent stem cells] are expanded in culture.”

The safety of patients comes first

Senior authors on the study, Dr. Jeanne Loring from TSRI and Dr. Nicholas Schork from JCVI, explained in a TSRI News Release that the goal of this study was to make sure that the reprogramming methods used to make iPS cells were safe for patients.

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Jeanne Loring

“We wanted to know whether reprogramming cells would make the cells prone to mutations,” said Jeanne Loring, “The answer is ‘no.’ The methods we’re using to make pluripotent stem cells are safe.”

 

Nicholas Schork added:

Nicholas Schork

Nicholas Schork

“The safety of patients comes first, and our study is one of the first to address the safety concerns about iPSC-based cell replacement strategies and hopefully will spark further interest.”

 

 

Moving from bench to clinic

It’s good news that reprogramming methods are relatively safe, but the fact that maintaining and expanding iPS cells in culture causes cancerous mutations is still a major issue that scientists need to address.

Jeanne Loring recognizes this important issue and says that the next steps are to use similar genomic analyses to assess the safety of reprogrammed iPS cells before they are used in patients.

“We need to move on to developing these cells for clinical applications,” said Loring. “The quality control we’re recommending is to use genomic methods to thoroughly characterize the cells before you put them into people.”

CIRM-funded team traces molecular basis for differences between human and chimp face

So similar yet so different
Whenever I go to the zoo, I could easily spend my entire visit hanging out with our not-so-distant relatives, the chimpanzees. To say we humans are similar to them is quite an understatement. Sharing 96% of our DNA, chimps are more closely related to us than they are to gorillas. And when you just compare our genes – that is, the segments of DNA that contain instructions for making proteins – we’re even more indistinguishable.

Chimps and Humans: So similar yet so different

Chimps and Humans: So similar yet so different

And yet you wouldn’t mistake a human for a chimp. I mean, I do have hairy arms, but they’re not that hairy. So what accounts for our very different appearance if our genes are so similar?

To seek out answers, a CIRM-funded team at Stanford University used both human and chimp induced pluripotent stem cells (iPSCs) to derive cranial neural crest cells (CNCCs). This cell type plays a key role in shaping the overall structure of the face during the early stages of embryo development. In a report published late last week in Cell, the team found differences, not in the genes themselves, but in gene activity between the human and chimp CNCCs.

Enhancers: Volume controls for your genes
Pinpointing the differences in gene activity relied on a comparative analysis of so-called enhancer regions of human and chimp DNA. Unlike genes, the enhancer regions of DNA do not provide instructions for making proteins. Instead they dictate how much protein to make by acting like volume control knobs for specific genes. A particular volume level, or gene activity, is determined by specific combinations of chemical tags and DNA-binding proteins on an enhancer region of DNA.

Enhancers: DNA segments that act like a volume control know for gene activity (Image source: xxxx)

Enhancers: DNA segments that act like a volume control knobs for gene activity (Image source: FANTOM Project, University of Copenhagen)

The researchers used several sophisticated lab techniques to capture a snapshot of this enhancer tagging and binding in the CNCCSs. They mostly saw similarities between human and chimp enhancers but, as senior author Joanna Wysocka explains in a Stanford University press release, they did uncover some differences:

“In particular, we found about 1,000 enhancer regions that are what we termed species-biased, meaning they are more active in one species or the other. Interestingly, many of the genes with species-biased enhancers and expression have been previously shown to be important in craniofacial development.”

PAX Humana: A genetic basis for our smaller jawline and snout?
For example, their analysis revealed that the genes PAX3 and PAX7 are associated with chimp-biased enhancer regions, and they had higher levels of activity in chimp CNCCs. These results get really intriguing once you learn a bit more about the PAX genes: other studies in mice have shown that mutations interfering with PAX function lead to mice with smaller, lower jawbones and snouts. So the lower level of PAX3/PAX7 gene activity in humans would appear to correlate with our smaller jaws and snout (mouth and nose) compared to chimps. Did that just blow your mind? How about this:

The researchers also found a variation in the enhancer region for the gene BMP4. But in this case, BMP4 was highly related to human-biased enhancer regions and had higher activity in humans compared to chimps. Previous mouse studies have shown that forcing higher levels of BMP4 specifically in CNCCs leads to shorter lower and upper jawbones, rounder skulls, and eyes positioned more to the front of the face. These changes caused by BMP4 sound an awful lot like the differences in human and chimp facial structures. It appears the Stanford group has established a terrific strategy for tracing the genetic basis for differences in humans and chimps.

So what’s next? According to Wysocka, the team is digging deeper into their data:

“We are now following up on some of these more interesting species-biased enhancers to better understand how they impact morphological differences. It’s becoming clear that these cellular pathways can be used in many ways to affect facial shape.”

And in the bigger picture, the researchers also suggest that this “cellular anthropology” approach could also be applied to a human to human search for DNA enhancer regions that play a role in the variation between healthy and disease states.

Throwback Thursday: Progress to a Cure for ALS

Welcome to our new “Throwback Thursday” (TBT) series. CIRM’s Stem Cellar blog has a rich archive of stem cell content that is too valuable to let dust bunnies take over.  So we decided to brush off some of our older, juicy stories and see what advancements in stem cell research science have been made since!

ALS is also called Lou Gehrig's disease, named after the famous American baseball player.

ALS is also called Lou Gehrig’s disease, named after the famous American baseball player.

This week, we’ll discuss an aggressive neurodegenerative disease called Amyotrophic Lateral Sclerosis or ALS. You’re probably more familiar with its other name, Lou Gehrig’s disease. Gehrig was a famous American Major League baseball player who took the New York Yankees to six world championships. He had a gloriously successful career that was sadly cut short by ALS. Post diagnosis, Gehrig’s physical performance quickly deteriorated, and he had to retire from a sport for which he was considered an American hero. He passed away only a year later, at the young age of 37, after he succumbed to complications caused by ALS.

A year ago, we published an interesting blog on this topic. Let’s turn back the clock and take a look at what happened in ALS research in 2014.

TBT: Disease in a Dish – Using Human Stem Cells to Find ALS Treatments

This blog featured the first of our scintillating “Stem Cells in Your face” video series called “Treating ALS with a Disease in a Dish.” Here is an excerpt:

Our latest video Disease in a Dish: That’s a Mouthful takes a lighthearted approach to help clear up any head scratching over this phrase. Although it’s injected with humor, the video focuses on a dreadful disease: amyotrophic lateral sclerosis (ALS). Also known as Lou Gehrig’s disease, it’s a disorder in which nerve cells that control muscle movement die. There are no effective treatments and it’s always fatal, usually within 3 to 5 years after diagnosis.

To explain disease in a dish, the video summarizes a Science Translation Medicine publication of CIRM-funded research reported by the laboratory of Robert Baloh, M.D., Ph.D., director of Cedars-Sinai’s multidisciplinary ALS Program. In the study, skin cells from patients with an inherited form of ALS were used to create nerve cells in a petri dish that exhibit the same genetic defects found in the neurons of ALS patients. With this disease in a dish, the team identified a possible cause of the disease: the cells overproduce molecules causing a toxic buildup that affects neuron function. The researchers devised a way to block the toxic buildup, which may point to a new therapeutic strategy.

New Stem Cell Discoveries in ALS Make Progress to Finding a Cure

So what’s happened in the field of ALS research in the past year? I’m happy to report that a lot has been accomplished to better understand this disease and to develop potential cures! Here are a few highlights that we felt were worth mentioning:

  • The Ice Bucket Challenge launched by the ALS Association is raising awareness and funds for ALS research.

    The Ice Bucket Challenge launched by the ALS Association is raising awareness and funds for ALS research.

    Ice Bucket Challenge. The ALS Association launched the “world’s largest global social media phenomenon” by encouraging brave individuals to dump ice-cold water on their heads to raise awareness and funds for research into treatments and cures for ALS. This August, the ALS Association re-launched the Ice Bucket Challenge campaign in efforts to raise additional funds and to make this an annual event.

  • ALS Gene Mapping. In a story released yesterday, the global biotech company Biogen is partnering with Columbia University Medical Center to map ALS disease genes. An article from Bloomberg Business describes how using Ice Bucket Money to create “a genetic map of the disease may help reveal the secrets of a disorder that’s not well understood, including how much a person’s genes contribute to the likelihood of developing ALS.” Biogen is also launching a clinical trial for a new ALS drug candidate by the end of the year.
  • New Drug target for ALS. Our next door neighbors at the Gladstone Institutes here in San Francisco published an exciting new finding in the journal PNAS in June. In collaboration with scientists at the University of Michigan, they discovered a new therapeutic target for ALS. They found that a protein called hUPF1 was able to protect brain cells from ALS-induced death by preventing the accumulation of toxic proteins in these cells. In a Gladstone press release, senior author Steve Finkbeiner said, “This is the first time we’ve been able to link this natural monitoring system to neurodegenerative disease. Leveraging this system could be a strategic therapeutic target for diseases like ALS and frontotemporal dementia.”
  • Stem cells, ALS, and clinical trials. Clive Svendsen at Cedars-Sinai is using gene therapy and stem cells to develop a cure for ALS. His team is currently working in mice to determine the safety and effectiveness of the treatment, but they hope to move into clinical trials with humans by the end of the year. For more details, check out our blog Genes + Cells: Stem Cells deliver genes as drugs and hope for ALS.

These are only a few of the exciting and promising stories that have come out in the past year. It’s encouraging and comforting to see, however, that progress towards a cure for ALS is definitely moving forward.

One-Time, Lasting Treatment for Sickle Cell Disease May be on Horizon, According to New CIRM-Funded Study

For the nearly 1,000 babies born each year in the United States with sickle cell disease, a painful and arduous road awaits them. The only cure is to find a bone marrow donor—an exceedingly rare proposition. Instead, the standard treatment for this inherited blood disorder is regular blood transfusions, with repeated hospitalizations to deal with complications of the disease. And even then, life expectancy is less than 40 years old.

In Sickle Cell Disease, the misshapen red blood cells cause painful blood clots and a host of other complications.

In Sickle Cell Disease, the misshapen red blood cells cause painful blood clots and a host of other complications.

But now, scientists at UCLA are offering up a potentially superior alternative: a new method of gene therapy that can correct the genetic mutation that causes sickle cell disease—and thus help the body on its way to generate normal, healthy blood cells for the rest of the patient’s life. The study, funded in part by CIRM and reported in the journal Blood, offers a great alternative to developing a functional cure for sickle cell disease. The UCLA team is about to begin a clinical trial with another gene therapy method, so they—and their patients—will now have two shots on goal in their effort to cure the disease.

Though sickle cell disease causes dangerous changes to a patient’s entire blood supply, it is caused by one single genetic mutation in the beta-globin gene—altering the shape of the red blood cells from round and soft to pointed and hard, thus resembling a ‘sickle’ shape for which the disease is named. But the UCLA team, led by Donald Kohn, has now developed two methods that can correct the harmful mutation. As he explained in a UCLA news release about the newest technique:

“[These results] suggest the future direction for treating genetic diseases will be by correcting the specific mutation in a patient’s genetic code. Since sickle cell disease was the first human genetic disease where we understood the fundamental gene defect, and since everyone with sickle cell has the exact same mutation in the beta-globin gene, it is a great target for this gene correction method.”

The latest gene correction technique used by the team uses special enzymes, called zinc-finger nucleases, to literally cut out and remove the harmful mutation, replacing it with a corrected version. Here, Kohn and his team collected bone marrow stem cells from individuals with sickle cell disease. These bone marrow stem cells would normally give rise to sickle-shaped red blood cells. But in this study, the team zapped them with the zinc-finger nucleases in order to correct the mutation.

Then, the researchers implanted these corrected cells into laboratory mice. Much to their amazement, the implanted cells began to replicate—into normal, healthy red blood cells.

Kohn and his team worked with Sangamo BioSciences, Inc. to design the zinc-finger nucleases that specifically targeted and cut the sickle-cell mutation. The next steps will involve improving the efficiency and safest of this method in pre-clinical animal models, before moving into clinical trials.

“This is a promising first step in showing that gene correction has the potential to help patients with sickle cell disease,” said UCLA graduate student Megan Hoban, the study’s first author. “The study data provide the foundational evidence that the method is viable.”

This isn’t the first disease for which Kohn’s team has made significant strides in gene therapy to cure blood disorders. Just last year, the team announced a promising clinical trial to cure Severe Combined Immunodeficiency Syndrome, also known as SCID or “Bubble Baby Disease,” by correcting the genetic mutation that causes it.

While this current study still requires more research before moving into clinical trials, Kohn and his team announced last month that their other gene therapy method, also funded by CIRM, has been approved to start clinical trials. Kohn argues that it’s vital to explore all promising treatment options for this devastating condition:

“Finding varied ways to conduct stem cell gene therapies is important because not every treatment will work for every patient. Both methods could end up being viable approaches to providing one-time, lasting treatments for sickle cell disease and could also be applied to the treatment of a large number of other genetic diseases.”

Find Out More:
Read first-hand about Sickle Cell Disease in our Stories of Hope series.
Watch Donald Kohn speak to CIRM’s governing Board about his research.

Roadmap to our epigenome reveals the genetic switches that make one adult cell type different from others

A decade ago scientists made a huge news splash when they announced the completion of the human genome project declaring it the first road map of our genes. But it did not take long to realize that the early road map was like some of the early days of GPS systems: it lacked knowledge of many on-ramps, off-ramps and one-way streets.

Today, the scientific world announced a massive fix to its genetic GPS. While all of our cells carry the same genes, their function varies wildly based one which genes are turned off, which are turned on, and even which are turned on in a hyper active way. Complex chemical and structural changes in the chromosomes that house our genes—collectively called the epigenome—determine that activity.

This video from Nature explaining the epigenome with music metaphors is linked in the last paragraph.

This video from Nature explains the epigenome with music metaphors.


A massive project, mostly funded by the National Institutes of Health through a consortium of research teams around the country, published a series of papers today in Nature. The Roadmap Epigenomic Consortium did extensive analysis of 111 epigenomes from different types of cells: normal heart tissue and immune cells, for example, as well as cells from patients with diseases such as neurons from patients with Alzheimer’s. The Scientist this morning quoted one member of the Consortium, MIT’s Manolis Kellis:

“The human epigenome is this collection of . . . chemical modifications on the DNA itself and on the packaging that holds DNA together. All our cells have a copy of the same book, but they’re all reading different chapters, bookmarking different pages, and highlighting different paragraphs and words.”

CIRM funding contributed to two of the papers authored by a team at the University of California, San Diego. One of the papers looked at how the genetic structure of stem cells changes as they mature and differentiate into specific types of adult tissue. The other looked at how structural differences determine which of the chromosomes we inherit—the one from mom or the one from dad—has a stronger influence on specific traits. The senior author on the studies, Bing Ren, noted in a university press release that these differences will be important as we think about individualizing therapies:

“Both of these studies provide important considerations for clinicians and researchers who are developing personalized medicines based on a patient’s genomic information”

The consortium’s publications today resulted from a massive data analysis. A press release from the Broad Institute in Cambridge, Massachusetts, describes the effort that required grouping two million predicted areas of change in the chromosomes into 200 sets or modules and then looking for how those modules impacted different cell types.

But if you are still having trouble understanding the concept of the epigenome, I highly recommend taking the five minutes it takes to watch this video produced by Nature. It equates the process to a symphony and what occurs when you change notes and intensity in the score.

All Things Being (Un)Equal: Scientists Discover Gene that Breaks Traditional Laws of Inheritance

One of the most fundamental laws of biology is about to be turned on its head, according to new research from scientists at the University of North Carolina (UNC) School of Medicine.

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As reported in the journal PLOS Genetics, UNC researchers identified a gene that does not obey traditional laws that determine how genes get passed down from parents to offspring. In experiments on laboratory mice, they found a gene called R2d2 causes female mice to pass on more genetic information than the males did—an observation that appears to contradict principles of genetic inheritance set forth more than a century ago.

As you may (or may not) remember from freshmen biology class, the laws of inheritance were laid down by the 19th century monk Gregor Mendel. Through meticulous observations of his garden’s pea plants, he found that each parent contributes their genetic information equally to their offspring.

But 150 years of scientific discovery later, scientists have discovered that this isn’t always the case.

Instead, in some cases one of the parents will contribute a greater percentage of genetic information than the other, a process called meiotic drive. Scientists had seen evidence of this process occurring in mammals for quite some time, but hadn’t narrowed down the driver of the process to a particular gene. According to UNC researchers, R2d2 is that gene. Senior author Fernando Pardo-Manuel de Villena explains:

“R2d2 is a good example of a poorly understood phenomenon known as female meiotic drive—when an egg is produced and a ‘selfish gene’ is segregated to the egg more than half the time.”

Pardo-Manuel de Villena notes that one example of this process occurs during trisomies—when three chromosomes (two from one parent and one from the other) are passed down to the embryo. The most common trisomy, trisomy 21, is more commonly known as Down Syndrome.

With these findings, Pardo-Manuel de Villena and the team are hoping to gain important insights into the underlying cause of trisomies, as well as the underlying causes for miscarriage—which are often not known.

“Understanding how meiotic drive works may shed light on the … abnormalities underlying these disorders,” said Pardo-Manuel de Villena.

This research was performed in large part by first author John Didion, who first discovered R2d2 when breeding two different types of mice for genetic analysis. Using whole-genome sequencing of thousands of laboratory mice, Didion and his colleagues saw that genes were passed down equally from each mouse’s parents. But a small section, smack dab in the middle of chromosome 2, was different.

Further analysis revealed that this section of chromosome 2 had a disproportionately larger number of genes from the mouse’s mother, compared to its father—showing a clear example of female meiotic drive. And at the heart of it all, Didion discovered, was the R2d2 gene.

The UNC team are already busy diving deeper into the relationship between R2d2 and meiotic drive with a focus on understanding, and one day perhaps correcting, genetic abnormalities in the developing embryo.