Why having a wrinkled brain is a good thing

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We normally associate wrinkles with aging, such as wrinkled skin. But there’s one organ that is wrinkled right from the time we are born. It’s our brain. And new research shows those wrinkles are not a sign of age but are, in fact, a sign of just how large and complex our brains are.

The wrinkles, according to U.C. Santa Barbara (UCSB) postdoctoral scholar Eyal Karzbrun, are vital to our development because they create a greater surface area giving our neurons, or brain nerve cells, more space to create connections and deliver information.

In an article in UCSB’s Daily Nexus, Karzbrun says while our knowledge of the brain is increasing there are still many things we don’t understand:

“The brain is a complex organ whose organization is essential to its function. Yet it is ‘assembled by itself’. How this assembly takes place and what physics come into play is fundamental to our understanding of the brain.”

Eyal Karzbrun

Eyal Karzbrun: Photo courtesy UCSB

Karzbrun used stem cells to create 3D clusters of brain cells, to better understand how they organize themselves. He said brains are like computers in the way they rely on surface area to process information.

“In order to be computationally strong and quick, what your brain does is take a lot of surface area and put it in a small volume. The cerebral cortex, which occupies most of the volume in your brain, has a unique architecture in which neurons are layered on the outer surface of the brain, and the bulk of the brain is composed of axons, [or] biological wire which interconnect the neurons.”

Karzbrun says gaining a deeper understanding of how the brain is formed, and why it takes the shape it does, may help us develop new approaches to treating problems in the brain.

 

Research Targeting Prostate Cancer Gets Almost $4 Million Support from CIRM

Prostate cancer

A program hoping to supercharge a patient’s own immune system cells to attack and kill a treatment resistant form of prostate cancer was today awarded $3.99 million by the governing Board of the California Institute for Regenerative Medicine (CIRM)

In the U.S., prostate cancer is the second most common cause of cancer deaths in men.  An estimated 170,000 new cases are diagnosed each year and over 29,000 deaths are estimated in 2018.  Early stage prostate cancer is usually managed by surgery, radiation and/or hormone therapy. However, for men diagnosed with castrate-resistant metastatic prostate cancer (CRPC) these treatments often fail to work and the disease eventually proves fatal.

Poseida Therapeutics will be funded by CIRM to develop genetically engineered chimeric antigen receptor T cells (CAR-T) to treat metastatic CRPC. In cancer, there is a breakdown in the natural ability of immune T-cells to survey the body and recognize, bind to and kill cancerous cells. Poseida is engineering T cells and T memory stem cells to express a chimeric antigen receptor that arms these cells to more efficiently target, bind to and destroy the cancer cell. Millions of these cells are then grown in the laboratory and then re-infused into the patient. The CAR-T memory stem cells have the potential to persist long-term and kill residual cancer calls.

“This is a promising approach to an incurable disease where patients have few options,” says Maria T. Millan, M.D., President and CEO of CIRM. “The use of chimeric antigen receptor engineered T cells has led to impressive results in blood malignancies and a natural extension of this promising approach is to tackle currently untreatable solid malignancies, such as castrate resistant metastatic prostate cancer. CIRM is pleased to partner on this program and to add it to its portfolio that involves CAR T memory stem cells.”

Poseida Therapeutics plans to use the funding to complete the late-stage testing needed to apply to the Food and Drug Administration for the go-ahead to start a clinical trial in people.

Quest Awards

The CIRM Board also voted to approve investing $10 million for eight projects under its Discovery Quest Program. The Quest program promotes the discovery of promising new stem cell-based technologies that will be ready to move to the next level, the translational category, within two years, with an ultimate goal of improving patient care.

Among those approved for funding are:

  • Eric Adler at UC San Diego is using genetically modified blood stem cells to treat Danon Disease, a rare and fatal condition that affects the heart
  • Li Gan at the Gladstone Institutes will use induced pluripotent stem cells to develop a therapy for a familial form of dementia
  • Saul Priceman at City of Hope will use CAR-T therapy to develop a treatment for recurrent ovarian cancer

Because the amount of funding for the recommended applications exceeded the money set aside, the Application Subcommittee voted to approve partial funding for two projects, DISC2-11192 and DISC2-11109 and to recommend, at the next full Board meeting in October, that the projects get the remainder of the funds needed to complete their research.

The successful applications are:

 

APPLICATION

 

TITLE

 

INSTITUTION

CIRM COMMITTED FUNDING
DISC2-11131 Genetically Modified Hematopoietic Stem Cells for the

Treatment of Danon Disease

 

 

U.C San Diego

 

$1,393,200

 

DISC2-11157 Preclinical Development of An HSC-Engineered Off-

The-Shelf iNKT Cell Therapy for Cancer

 

 

U.C. Los Angeles

 

$1,404,000

DISC2-11036 Non-viral reprogramming of the endogenous TCRα

locus to direct stem memory T cells against shared

neoantigens in malignant gliomas

 

 

U.C. San Francisco

 

$900,000

DISC2-11175 Therapeutic immune tolerant human islet-like

organoids (HILOs) for Type 1 Diabetes

 

 

Salk Institute

 

$1,637,209

DISC2-11107 Chimeric Antigen Receptor-Engineered Stem/Memory

T Cells for the Treatment of Recurrent Ovarian Cancer

 

 

City of Hope

 

$1,381,104

DISC2-11165 Develop iPSC-derived microglia to treat progranulin-

deficient Frontotemporal Dementia

 

 

Gladstone Institutes

 

$1,553,923

DISC2-11192 Mesenchymal stem cell extracellular vesicles as

therapy for pulmonary fibrosis

 

 

U.C. San Diego

 

$865,282

DISC2-11109 Regenerative Thymic Tissues as Curative Cell

Therapy for Patients with 22q11 Deletion Syndrome

 

 

Stanford University

 

$865,282

 

 

Headline: Stem Cell Roundup: Here are some stem cell stories that caught our eye this past week.

In search of a miracle

Jordan and mother

Luane Beck holds Jordan in the emergency room while he suffers a prolonged seizure. Jordan’s seizures sometimes occur one after another with no break, and they can be deadly without emergency care. Photo courtesy San Francisco Chronicle’s Kim Clark

One of the toughest parts of my job is getting daily calls and emails from people desperate for a stem cell treatment or cure for themselves or a loved one and having to tell them that I don’t know of any. You can hear in their voice, read it in their emails, how hard it is for them to see someone they love in pain or distress and not be able to help them.

I know that many of those people may think about turning to one of the many stem cell clinics, here in the US and in Mexico and other countries, that are offering unproven and unapproved therapies. These clinics are offering desperate people a sense of hope, even if there is no evidence that the therapies they provide are either safe or effective.

And these “therapies” come with a big cost, both emotional and financial.

The San Francisco Chronicle this week launched the first in a series of stories they are doing about stem cells and stem cell research, the progress being made and the problems the field still faces.

One of the biggest problems, are clinics that offer hope, at a steep price, but no evidence to show that hope is justified. The first piece in the Chronicle series is a powerful, heart breaking story of one mother’s love for her son and her determination to do all she can to help him, and the difficult, almost impossible choices she has to make along the way.

It’s called: In search of a miracle.

A little turbulence, and a French press-like device, can help boost blood platelet production

Every year more than 21 million units of blood are transfused into people in the US. It’s a simple, life-saving procedure. One of the most important elements in transfusions are  platelets, the cells that stop bleeding and have other healing properties. Platelets, however, have a very short shelf life and so there is a constant need to get more from donors. Now a new study from Japan may help fix that problem.

Platelets are small cells that break off much larger cells called megakaryocytes. Scientists at the Center for iPS Cell Research and Application (CiRA) created billions of megakaryocytes using iPS technology (which turns ordinary cells into any other kind of cell in the body) and then placed them in a bioreactor. The bioreactor then pushed the cells up and down – much like you push down on a French press coffee maker – which helped promote the generation of platelets.

In their study, published in the journal Cell, they report they were able to generate 100 billion platelets, enough to be able to treat patients.

In a news release, CiRA Professor Koji Eto said they have shown this works in mice and now they want to see if it also works in people:

“Our goal is to produce platelets in the lab to replace human donors.”

Stem Cell Photo of the Week 

Photo Jul 11, 6 00 19 PM

Students at the CIRM Bridges program practice their “elevator pitch”. Photo Kyle Chesser

This week we held our annual CIRM Bridges to Stem Cell Research conference in Newport Beach. The Bridges program provides paid internships for undergraduate and masters-level students, a chance to work in a world-class stem cell research facility and get the experience needed to pursue a career in science. The program is training the next generation of stem cell scientists to fill jobs in California’s growing stem cell research sector.

This year we got the students to practice an “elevator Pitch”, a 30 second explanation, in plain English, of what they do, why they do it and why people should care. It’s a fun exercise but also an important one. We want scientists to be able to explain to the public what they are doing and why it’s important. After all, the people of California are supporting this work so they have a right to know, in language they can understand, how their money is changing the face of medicine.

Starving stem cells of oxygen can help build stronger bones

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J. Kent Leach: Photo courtesy UC Davis

We usually think that starving something of oxygen is going to make it weaker and maybe even kill it. But a new study by J. Kent Leach at UC Davis shows that instead of weakening bone defects, depriving them of oxygen might help boost their ability to create new bone or repair existing bone.

Leach says in the past the use of stem cells to repair damaged or defective bone had limited success because the stem cells often didn’t engraft in the bone or survive long if they did. That was because the cells were being placed in an environment that lacked oxygen (concentration levels in bone range from 3% to 8%) so the cells found it hard to survive.

However, studies in the lab had shown that if you preconditioned mesenchymal stem cells (MSCs), by exposing them to low oxygen levels before you placed them on the injury site, you helped prolong their viability. That was further enhanced by forming the MSCs into three dimensional clumps called spheroids.

Lightbulb goes off

In the  current study, published in Stem Cells, Leach says the earlier spheroid results  gave him an idea:

“We hypothesized that preconditioning MSCs in hypoxic (low oxygen) culture before spheroid formation would increase cell viability, proangiogenic potential (ability to create new blood vessels), and resultant bone repair compared with that of individual MSCs.”

So, the researchers placed one group of human MSCs, taken from bone marrow, in a dish with just 1% oxygen, and another identical group of MSCs in a dish with normal oxygen levels. After three days both groups were formed into spheroids and placed in an alginate hydrogel, a biopolymer derived from brown seaweed that is often used to build cellular cultures.

Seaweed

Brown seaweed

The team found that the oxygen-starved cells lasted longer than the ones left in normal oxygen, and the longer those cells were deprived of oxygen the better they did.

Theory is great, how does it work in practice?

Next was to see how those two groups did in actually repairing bones in rats. Leach says the results were encouraging:

“Once again, the oxygen-deprived, spheroid-containing gels induced significantly more bone healing than did gels containing either preconditioned individual MSCs or acellular gels.”

The team say this shows the use of these oxygen-starved cells could be an effective approach to repairing hard-to-heal bone injuries in people.

“Short‐term exposure to low oxygen primes MSCs for survival and initiates angiogenesis (the development of new blood vessels). Furthermore, these pathways are sustained through cell‐cell signaling following spheroid formation. Hypoxic (low oxygen) preconditioning of MSCs, in synergy with transplantation of cells as spheroids, should be considered for cell‐based therapies to promote cell survival, angiogenesis, and bone formation.”

CIRM & Dr. Leach

While CIRM did not fund this study we have invested more than $1.8 million in another study Dr. Leach is doing to develop a new kind of imaging technology that will help us see more clearly what is happening in bone and cartilage-targeted therapies.

In addition, back in March of 2012, Dr. Leach spoke to the CIRM Board about his work developing new approaches to growing bone.

 

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

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

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

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

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

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

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

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

 

Stem cell gene therapy combination could help children battling a rare genetic disorder

Hunter Syndrome-2

A child with Hunter Syndrome

Hunter syndrome is devastating. It’s caused by a single enzyme, IDS, that is either missing or malfunctioning. Without the enzyme the body is unable to break down complex sugar molecules and as those build up they cause permanent, progressive damage to the body and brain and, in some instances, result in severe mental disabilities. There is no cure and existing treatments are limited and expensive.

But now researchers at the University of Manchester in England have developed an approach that could help children – the vast majority of them boys – suffering from Hunter syndrome.

Working with a mouse model of the disease the researchers took some blood stem cells from the bone marrow and genetically re-engineered them to correct the mutation that caused the problem. They also added a “tag” to the IDS enzyme to help it more readily cross the blood brain barrier and deliver the therapy directly to the brain.

In a news release Brian Bigger, the lead researcher of the study published in EMBO Molecular Medicine, said the combination therapy helped correct bone, joint and brain disease in the mice.

“We expected the stem cell gene therapy approach to deliver IDS enzyme to the brain, as we have shown previously for another disease: Sanfilippo types A and B, but we were really surprised to discover how much better the tag made the therapy in the brain. It turns out that the tag didn’t only improve enzyme uptake across the blood brain barrier, but also improved uptake of the enzyme into cells and it appeared to be more stable in the bloodstream – all improvements on current technology.”

While the results are very encouraging it is important to remember the experiment was done in mice. So, the next step is to see if this might also work in people.

Joshua Davies has made a video highlighting the impact Hunter syndrome has on families: it’s called ‘Living Beyond Hope’

“Junk” DNA is development gold for the dividing embryo

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

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

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

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

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

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

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

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

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

Fish umbrellas and human bone: protecting blood stem cells from the sun’s UV rays

Blood stem cells.jpg

Most people probably do not question the fact that human blood stem cells – those that give rise to all the cells in our blood – live inside the marrow of our bones, called a stem cell “niche”. But it is pretty odd when you stop to think about it. I mean, it makes sense that the hard, calcium-rich structure of bones provide our bodies with a skeleton but why is it also responsible for making our blood?

This week, researchers at Harvard report in Nature that the answer may come down to protecting these precious cells from the DNA-damaging effects of UV radiation from the sun. They arrived at those insights by examining zebrafish which harbor blood stem cells, not in their bones, but in their kidneys. Fredrich Kapp, MD, the first author of the report, was trying to analyze blood stem cells in zebrafish under the microscope but noticed a layer of other cells on top of the kidney was obscuring his view.

fishumbrella

In a zebrafish larva (illustration above), a dark umbrella formed by pigmented cells (white arrows point to these black spots in box, left) in the kidney protects vulnerable stem cells from damaging UV light. Right image is a closeup of the box. Scale bars equal 100 micrometers (left) and 50 micrometers (right). Credit: F. Kapp et al./Nature 2018
Read more at: https://phys.org/news/2018-06-blood-cells-bones.html#jCp

That layer of cells turned out to be melanocytes which produce melanin a pigment that gives our skin color. Melanin also protects our skin cells from the sun’s UV radiation which damages our DNA and can cause genetic mutations. In a press release, Kapp recalled his moment of insight:

“The shape of the melanocytes above the kidney reminded me of a parasol, so I thought, do they provide UV protection to blood stem cells?”

To answer his question, he and his colleagues compared the effects of UV radiation on normal zebrafish versus mutant zebrafish lacking the layer of melanocytes. Confirming Kapp’s hypothesis, the fish missing the melanocyte layer had fewer blood stem cells. Simply turning the normal fish upside down and exposing them to the UV rays also depleted the blood stem cells.

And here’s where the story gets really cool. In studying frogs – animals closer to us on the evolutionary tree – they found that as the tadpole begins to grow legs, their blood stem cells migrate from the melanocyte-covered kidney cells to inside the bone marrow, an even better form of UV protection. Senior author Leonard Zon explained the importance of this finding:

“We now have evidence that sunlight is an evolutionary driver of the blood stem cell niche. As a hematologist and oncologist, I treat patients with blood diseases and cancers. Once we understand the niche better, we can make blood stem cell transplants much safer.”

 

 

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

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

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Pumping up our knowledge about muscle stem cells

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

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

In a press release, Dr. Kioussi said:

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Chrissa Kioussi, PhD

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

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

Using biological “codes” to generate neurons in a dish

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

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

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

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

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

KristinBaldwin

Kristin Baldwin, PhD

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

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