by Nivanthika K. Wimalasena
figures by Anna Maurer

Imagine you could know everything you needed to make you into exactly who you were destined to be—which books would inspire you, which people you needed to meet, what you should study in school. Scientists are trying to understand exactly that for the life of a stem cell. They are using their understanding of stem cells and the way they develop into other types of cells in the body to study complex disorders of the brain. By making stem cells into specific types of neurons and mini brain-like structures called organoids, scientists are making major progress toward treating and understanding disease.

Reprogramming the Cell: How to Make a Stem Cell

Stem cells, the forefathers of each of the 3.72 trillion cells that make up the adult human body, have the unique ability to become any kind of cell, much like the potential we begin with in life. They slowly make choices that propel them down certain paths, toward certain fates, until ultimately they mature and end up as a neuron in your brain, or a skin cell in your toe, or a muscle cell in your heart. Throughout human development, the fate of most stem cells becomes narrower and more specific until they reach a fully mature state, a process known as differentiation (Figure 1). Within the body, the process of differentiation is generally irreversible: —once a mature cell is formed, it no longer has unlimited potential, or pluripotency.

Figure 1: The process of differentiation as it occurs in the body. Pluripotent stem cells give rise to different mature cell types, including neurons.

In 2006, Shinya Yamanaka and colleagues made a discovery that has advanced our understanding of stem cells and has allowed scientists to defy this natural pattern. Scientists previously thought that inducing mature cells to become stem cells again would require many difficult steps, much like trying to get an adult to revert to a child-like state. However, Yamanaka stunningly showed scientists could add only four proteins, now known as the Yamanaka factors, to start a series of events in mature cells to cause them to become immature stem cells, a process known as reprogramming (Figure 2). Stem cells created in this way have their singular property of being able to differentiate into any type of cell, and are therefore known as induced pluripotent stem cells, or iPScs.  Because of this Nobel Prize-winning work, we can now take mature skin or blood cells and induce them to revert back to their original state as a stem cell, essentially erasing the decisions they previously made and allowing them to start over.

Opening the Black Box: A New Way to Study the Human Brain

For scientists trying to understand disease, stem cell technology is revolutionary in cases in which human tissue is not available for study in another form. For example, neurons, the nerve cells that make up the brain, are nearly impossible to obtain from living patients because of the risk of damaging the brain. Using the methods described above, a scientist can take skin cells from a donor and transform them into neurons that contain the same DNA as the donor, thereby creating neurons “from that person,” known as iPS-derived neurons. This means that a patient with a neurological condition like ALS (amyotrophic lateral sclerosis – also known as Lou Gehrig’s disease) or schizophrenia can donate their skin cells to enable scientists to create “ALS neurons” or “schizophrenic neurons.” This technique has incredible potential to help us understand and perhaps treat neurological diseases.

For example, ALS is an illness that leads to the death of motor neurons, the cells that transmit signals between our brains and our bodies, allowing us to flex, extend and otherwise control our muscles. These are the only cells that die in ALS, and when they do, it leads to muscle weakness, paralysis, and eventually death. Therefore, to use iPSc-derived neurons to understand this disease, scientists first needed to learn how to specifically make motor neurons from patients with ALS, a significant undertaking.

Figure 2. The process of reprogramming mature skin cells to revert to a pluripotent state (left). The process of using iPS cells generated through reprogramming to make patient-specific ALS neurons and brain organoids.
Figure 2: The process of reprogramming mature skin cells to revert to a pluripotent state (left). The process of using iPS cells generated through reprogramming to make patient-specific ALS neurons and brain organoids.

Directed Differentiation: How to Make a Neuron

Transforming patient stem cells into the right type of cell is one of the major hurdles in trying to understand a disease. Scientists need to understand what factors led a given type of cell to become what it is. This task would be like scientists looking at a person and working backwards to understand what influenced them to make the choices that transformed them into their adult self. As you can imagine, this is no easy feat; however, once scientists know what these factors are, they can artificially introduce them in a process known as directed differentiation, effectively biasing iPScs to the fate of interest (Figure 2).

By comparing motor neurons from ALS patients to motor neurons from healthy people, scientists can try to uncover the differences between “sick” and healthy cells, and can also test drugs to see whether a given drug can make neurons from an ALS patient look and behave more like neurons from a healthy person. However, while this approach of making a specific, known cell type shows great promise for tackling diseases like ALS, many neurological disorders affect cell types that scientists have not been able to make, or they alter the brain as a whole rather than specific types of neurons.

One such condition is microcephaly, which has recently gained attention because of its association with Zika virus. Microcephaly is a condition in which infants are born with abnormally small brains because of a defect in the patterning and migration of many of the types of cells that form the brain. This can cause a variety of neurological problems including seizures, sensory deficits, and intellectual disability. Traditionally, microcephaly has been hard to study because it is difficult to model in mice and other animals and because many different cell types are affected. However, organoids, a new application of stem cell technology, are opening up potential avenues for research.

Organoids: Brains in a Dish?

Organoids are made via an abbreviated version of more traditional directed differentiation. Instead of trying to replicate all of the choices that lead an iPSc to a specific fate, scientists introduce a few initial factors that bias the cells and then let them self-organize naturally (Figure 2). It might be like narrowing your career choices by choosing a college major—you’ve chosen a general path, but you could still choose any number of career options based on the kinds of opportunities you encounter. Analogously, brain organoids are made from iPS cells by introducing factors that bias stem cells to become neuronal, but then letting them differentiate independently based on the local cues in their environments. The result is a mini brain-like structure with complex layers of different kinds of neurons, as seen in the fully developed brain. To apply this to microcephaly, scientists have made iPS cell lines from patients and formed “microcephalic” organoids, so that they can better understand the specific processes that are abnormal in the development of microcephalic brains.

The Promise of iPS-derived Neurons and the Challenges Ahead

Ultimately, iPS-derived neurons show a great deal of promise in understanding and treating a variety of diseases and disorders. However, there are still some caveats to these approaches. While the technology is improving for creating specific types of neurons, it is often difficult to confirm that neurons created in the lab are biologically the same as the neurons in the patient they came from. There are concerns about whether important information, such as DNA modification, is lost in the process of converting mature cells back into stem cells, and whether this information could be contributing to the diseases scientists are trying to understand. Additionally, some aspects of disease, such as aging are hard to replicate in a dish, making the process of studying Alzheimer’s disease and other forms of dementia difficult.

As these issues are being studied, iPS technology is improving and pushing the boundaries of science and medicine. In addition to understanding ALS and microcephaly, scientists are working on making neurons for transplantation into people with paralyzing nerve injuries from accidents or nerve loss from disorders like Parkinson’s disease. These neurons are being used to study complex psychiatric disorders like depression, autism, and schizophrenia, which are still poorly understood and difficult to model in other ways. Ultimately, these cells have opened the door to study the human brain in a way that was not previously possible. Rather than relying on the brains of more primitive mammals or post-mortem samples from humans, we can now study living human neurons. We are moving toward understanding not only how they are made in the body, but also how they are altered in disease, and remarkably, how we can use them to improve the health of millions.

Nivanthika K. Wimalasena is a PhD student in the Program in Neuroscience at Harvard Medical School.

This article is part of the April 2016 Special Edition on Neurotechnology.

Further reading:

The original paper on Yamanaka factors and iPS cells

More information about the potential of iPS cells

More information on different types of organoids

Cover image is from AMNH and is a picture of a cerebral organoid.

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