Stem Cell Stories that Caught our Eye: finding the perfect match, imaging stem cells and understanding gene activity

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

LAPD officer in search of the perfect match.

LAPD Officer Matthew Medina with his wife, Angelee, and their daughters Sadie and Cassiah. (Family photo)

This week, the San Diego Union-Tribune featured a story that tugs at your heart strings about an LAPD officer in desperate need of a bone marrow transplant. Matthew Medina is a 40-year-old man who was diagnosed earlier this year with aplastic anemia, a rare disorder that prevents the bone marrow from producing enough blood cells and platelets. Patients with this disorder are prone to chronic fatigue and are at higher risk for infection and uncontrolled bleeding.

Matthew needs a bone marrow transplant to replace his diseased bone marrow with healthy marrow from a donor, but so far, he has yet to find a match. Part of the reason for this difficulty is the lack of diversity in the national bone marrow registry, which has over 25 million registered donors, the majority of which are white Americans of European decent. As a Filipino, Matthew has a 40% chance of finding a perfect match in the national registry compared to a 75% chance if he were white. An even more unsettling fact is that Filipinos make up less than 1% of donors on the national registry.

Matthew has a sister, but unfortunately, she wasn’t a match. For now, Matthew is being kept alive with blood transfusions at his home in Bellflower while he waits for good news. With the support of his family and friends, the hope is that he won’t have to wait for long. Already 1000 people in his local community have signed up to be bone marrow donors.

On a larger scale, organizations like A3M and Mixed Marrow are hoping to help patients like Matthew by increasing the diversity of the national bone marrow registry. A3M specifically recruits Asian donors while Mixed Match focuses on people with multi-ethnic backgrounds. Ayumi Nagata, a recruitment manager at A3M, said their main challenge is making healthy people realize the importance of being a bone marrow donor.

“They could be the cure for someone’s cancer or other disease and save their life. How often do we have that kind of opportunity?”

An algorithm that makes it easier to see stem cell development.

To understand how certain organs like the brain develop, scientists rely on advanced technologies that can track individual stem cells and monitor their fate as they mature into more specialized cells. Scientists can observe stem cell development with fluorescent proteins that light up when a stem cell expresses specific transcription factors that help decide the cell’s fate. Using a time-lapse microscope, these fluorescent stem cells can easily be identified and tracked throughout their lifetime.

But the pictures don’t always come out crystal clear. Just as a dirty camera lens makes for a dirty picture, images produced by time-lapse microscopy images can be plagued by shadows, artifacts and lighting inconsistencies, making it difficult to observe the orchestrated expression of transcription factors involved in a stem cell’s development.

This week in the journal Nature Communications, a team of scientists from Germany reported a solution that gives a clear view of stem cell development. The team developed a computer algorithm called BaSiC that acts like a filter and removes the background noise from time-lapse images of individual cells. Unlike previous algorithms, BaSiC requires fewer reference images to make its corrections.

The software BaSiC improves microscope images. (Credit: Tingying Peng / TUM/HMGU)

In coverage by Phys.org, author Dr. Tingying Peng explained the advantages of their algorithm,

“Contrary to other programs, BaSiC can correct changes in the background of time-lapse videos. This makes it a valuable tool for stem cell researchers who want to detect the appearance of specific transcription factors early on.”

The team proved that BaSiC is an effective image correcting tool by using it to study the development of hematopoietic or blood stem cells. They took time-lapse videos of blood stem cells over six days and observed that the stem cells chose between two developmental tracks that produced different types of mature blood cells. Using BaSiC, they found that blood stem cells that specialized into white blood cells expressed the transcription factor Pu.1 while the stem cells that specialized into red blood cells did not. Without the algorithm, they didn’t see this difference.

Senior author on the study, Dr. Nassir Navab, concluded by highlighting the importance of their technology and sharing his team’s vision for the future.

“Using BaSiC, we were able to make important decision factors visible that would otherwise have been drowned out by noise. The long-term goal of this research is to facilitate influencing the development of stem cells in a targeted manner, for example to cultivate new heart muscle cells for heat-attack patients. The novel possibilities for observation are bringing us a step closer to this goal.”

Silenced vs active genes: it’s like oil and water (Todd Dubicoff)

The DNA from just one of your cells would be an astounding six feet in length if stretched out end to end. To fit into a nucleus that is a mere 4/10,000th of an inch in diameter, DNA’s double helical structure is organized into intricate twists within twists with the help of proteins called histones.

Together the DNA and histones are called chromatin. And it turns out that chromatin isn’t just for stuffing all that genetic material into a tiny space. The amount of DNA folding also affects the regulation of genes. Areas of chromatin that are less densely packed are more accessible to DNA-binding proteins called transcription factors that activate gene activity. Other regions, called heterochromatin, are compacted which leads to silencing of genes because transcription factors are shut out.

But there’s a wrinkle in this story. More recently, scientists have shown that large proteins are able to wriggle their way into heterochromatin while smaller proteins cannot. So, there must be additional factors at play. This week, a CIRM-funded research project published in Nature provides a possible explanation.

Liquid-like fusion of heterochromatin protein 1a droplets is shown in the embryo of a fruit fly. (Credit: Amy Strom/Berkeley Lab)

Examining the nuclei of fruit fly embryos, a UC Berkeley research team report that various regions of heterochromatin coalesce into liquid droplets which physically separates them from regions where gene activity is high. This phenomenon, called phase-phase separation, is what causes oil droplets to fuse together when added to water. Lead author Dr. Amy Strom explained the novelty of this finding and its implications in a press release:

“We are excited about these findings because they explain a mystery that’s existed in the field for a decade. That is, if compaction [of chromatin] controls access to silenced [DNA] sequences, how are other large proteins still able to get in? Chromatin organization by phase separation means that proteins are targeted to one liquid or the other based not on size, but on other physical traits, like charge, flexibility, and interaction partners.”

Phase-phase separation can also affect other cell components, and problems with it have been linked to neurological disorders like dementia. In diseases like Alzheimer’s and Huntington’s, proteins aggregate causing them to become more solid than liquid over time. Strom is excited about how phase-phase separation insights could lead to novel therapeutic strategies:

“If we can better understand what causes aggregation, and how to keep things more liquid, we might have a chance to combat these types of disease.”

Measuring depression with non-invasive imaging of new brain cells

For most of the 20th century, scientists thought you’re basically stuck with the brain cells you’re born with. “Everything may die, nothing may be regenerated”, is how Santiago Ramón y Cajal, the father of modern neuroscience, described nerve cells, aka neurons, in the adult brain. But, over the past few decades, it’s become clear that stem cells are present in the brain and produce new neurons over the course of our lives.

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Hippocampus (in red)
Image: Life Science Databases

This better understanding of brain biology opened up new insights into brain function. For instance, a reduced volume of the hippocampus, an area of the brain important for learning and memory, is linked to depression and the use of anti-depressant drugs like Prozac have been shown to trigger the growth of new neurons in this part of the brain.

Now, researchers at the RIKEN institute in Japan have developed a non-invasive imaging method – so far, just in rats – to track the generation of new neurons from brain stem cells.  This study, reported in the Journal of Neuroscience, may provide new means to diagnose depression and to monitor the effectiveness of drugs in ways that aren’t currently possible.

A PET project to track new brain cells

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PET scan of human brain
Image: Wikipedia

The scientists focused on the use of positron emitting tomography (PET) imaging, which involves the injecting a radioactive tracer, designed to target an organ or a specific area of an organ, into the blood. The use of this type of tracer is routine in medical imaging and the radioactivity decays so fast that it’s essentially gone within 24 hours. The radioactive signal that’s emitted out from the body is then detected with PET scanning and reveals the precise location of the tracer within the body or organ. But PET scanning of neurogenesis in the brain had proved to be difficult – no definitive signals were observed. Magnetic resonance imaging (MRI) is also a no-go because it requires the risky injection of a tracer directly into the brain.

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PET scanner. Image: Jacoby Werther

The RIKEN team pinpointed the stumbling block: the lack of signal was due to the presence of proteins, called drug transporters, that continually pump the radioactive tracers out of the brain and back into the blood. When they re-ran the PET scan using a clinically available drug that blocks the transporter proteins, a neurogenesis signal was picked up.

Prozac helps stimulate new brain cell growth
With this obstacle overcome, the team tested out their technique. They gave one group of rats corticosterone, a stress hormone, for a month. This hormone is known to reduce neurogenesis and create depression-like behavior in the animals. They gave a second group of rats corticosterone plus Prozac. Sure enough, the PET scan signal was able to measure a decrease in neurogenesis in the corticosterone only group but also a recovery in neurogenesis in the group that received the hormone plus Prozac. Follow up analysis of rat brain slices confirmed that compared to untreated animals, neurogenesis was reduced 45% in the corticosterone group but no reduction was observed when Prozac was also included.

In a news release picked up by Nanowerk, team lead Yosky Kataoka discussed the game-changer possibilities of their new method:

“This is a very interesting finding because it has been a long-time dream to find a noninvasive test that can give objective evidence of depression and simultaneously show whether drugs are working in a given patient. We have shown that it is possible, at least in experimental animals, to use PET to show the presence of depression and the effectiveness of drugs… Since it is known that these same brain regions are involved in depression in the human brain, we would like to try this technique in the clinic and see whether it turns out to be effective in humans as well.”

Watch Spinal Cord Cells Take a Hike!

magic school busWhat exactly goes on inside the human body? If you asked this question to the children’s book character Ms. Frizzle, she would throw you into her Magic School Bus and take you on a wild ride “Inside the Human Body” to get you up close and personal with the different organs and structures within our bodies.

Ms. Frizzle had a wild imagination, but she was on to something with her crazy adventures. Recently, scientists took a page out of one of Ms. Frizzle children’s books and took their own wild ride to check out what’s going on with the human spinal cord.

In a paper published yesterday in Neuron, scientists from the Salk Institute in San Diego reported that they were able to watch spinal cord cells walk around the spine of mice in real-time. They used a special microscope that could track and record the movement of motor neurons, an important nerve cell that controls the movement of muscles in your body. What they found when they watched these cells was equivalent to a pot of gold at the end of the rainbow.

Check out their stunning movie here:

The scientists not only recorded the activity of these motor neurons, but they identified the other spinal cord cells that these neurons interact and make connections with. One of their most significant findings was a population of spinal cord cells that connected to a subtype of motor neurons to foster important muscle movements like walking.

Understanding how the different cells of the spinal cord work together is very important because it will allow scientists and doctors to figure out better ways to treat patients with spinal cord injuries or neurodegenerative diseases, like ALS, that affect motor neurons.

Senior author Samuel Pfaff commented in a press release on the importance of this study and how easy his team’s technology is to use:

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Samuel Pfaff

Using optical methods to be able to watch neuron activity has been a dream over the past decade. Now, it’s one of those rare times when the technology is actually coming together to show you things you hadn’t been able to see before. You don’t need to do any kind of post-image processing to interpret this. These are just raw signals you can see through the eyepiece of a microscope. It’s really a jaw-dropping kind of visualization for a neuroscientist.

While this study doesn’t provide a direct avenue for therapeutic development, it does pave the way for a better understanding of the normal, healthy processes that go on in the human spine. Having more knowledge of “what is right” will help scientists to develop better strategies to fix “what is wrong” in spinal cord injuries and diseases like ALS.


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Scientists Develop Colorful Cell-Imaging Technique

Proteins are the helmsmen of the cell. They drive the essential processes that keep cells alive, keep them healthy and keep them functioning. And in recent years scientists have discovered that proteins rarely act alone.

In fact, so-called ‘protein-protein interactions’ are now known to drive the vast majority of cellular functions. But figuring out exactly how they do so has proven difficult.

Luckily, scientists now have a way to see these interactions—in a dazzling array of Technicolor.

As described in today’s issue of Nature Methods, Robert Campbell and his team at the University of Alberta have announced a new way to visualize protein-protein interactions, by converting these interactions into changes in color. This technique could be employed across a variety of disciplines, helping scientists understand normal processes in the cell—and observe the molecular changes that occur when those processes go awry.

“With this development,” explained Campbell in a news release, “we can immediately image activity happening at the cellular level, offering an alternative to existing methods for detecting and imaging of protein-protein interactions in live cells.”

Called FPX, Campbell’s method links a change in a protein-protein interaction to a color. As seen in the video below, every time the interaction changes, a color change—from red to green, and back to red again—is visible.

The FPX method is based on previously published work by Campbell and others, which found that green and red fluorescent proteins could both be inserted into a single cell so that the protein could be red or green—but not both at the same time. So, the team was able to construct biosensors that changed color in response to changes in protein-protein interactions.

In this study, the researchers have essentially given scientists a powerful tool to help them understand how even the smallest molecular changes can lead to significant changes in the health of the cell.

According to Campbell:

“It will be immediately relevant to many areas of fundamental cell biology research and practical applications such as drug discovery. Ultimately, it will help researchers achieve breakthroughs in a wide variety of areas in the life sciences, such as neuroscience, diabetes and cancer.”