MIT Research News' Journal

Tissue architecture affects chromosome segregation

All growth and reproduction relies on a cell’s ability to replicate its chromosomes and produce accurate copies of itself. Every step of this process takes place within that cell.

Based on this observation, scientists have studied the replication and segregation of chromosomes as a phenomenon exclusively internal to the cell. They traditionally rely on warm nutritional cultures that promote growth but bear little resemblance to the cell’s external surroundings while in its natural environment.

New research by a group of MIT biologists reveals that this long-held assumption is incorrect. In a paper published this week, they describe how some types of cells rely on signals from surrounding tissue in order to maintain chromosome stability and segregate accurately.

Kristin Knouse, a fellow at the Whitehead Institute, is the lead author of the paper, which was published online in the journal Cell on Aug. 23. Angelika Amon, the Kathleen and Curtis Marble Professor in Cancer Research in the Department of Biology and a member of the Koch Institute for Integrative Cancer Research, is the senior author.

“The main takeaway from this paper is that we must study cells in their native tissues to really understand their biology,” Amon says. “Results obtained from cell lines that have evolved to divide on plastic dishes do not paint the whole picture.”

When cells replicate, the newly duplicated chromosomes line up within the cell and cellular structures pull one copy to each side. The cell then divides down the middle, separating one copy of each chromosome into each new daughter cell.

At least, that’s how it’s supposed to work. In reality, there are sometimes errors in the process of separating chromosomes into daughter cells, known as chromosome mis-segregation. Some errors simply result in damage to the DNA. Other errors can result in the chromosomes being unevenly divided between daughter cells, a condition called aneuploidy.

These errors are almost always harmful to cell development and can be fatal. In developing embryos, aneuploidy can cause miscarriages or developmental disorders such as Down syndrome. In adults, chromosome instability is seen in a large number of cancers.

To study these errors, scientists have historically removed cells from their surrounding tissue and placed them into easily controlled plastic cultures.

“Chromosome segregation has been studied in a dish for decades,” Knouse says. “I think the assumption was … a cell would segregate chromosomes the same way in a dish as it would in a tissue because everything was happening inside the cell.”

However, in previous work, Knouse had found that reported rates for aneuploidy in cells grown in cultures was much higher than the rates she found in cells that had grown within their native tissue. This prompted her and her colleagues to investigate whether the surroundings of a cell influence the accuracy with which that cell divided.

To answer this question, they compared mis-segregation rates between five different cell types in native and non-native environments.

But not all cells’ native environments are the same. Some cells, like those that form skin, grow in a very structured context, where they always have neighbors and defined directions for growth. Other cells, however, like cells in the blood, have greater independence, with little interaction with the surrounding tissue.

In the new study, the researchers observed that cells that grew in structured environments in their native tissues divided accurately within those tissues. But once they were placed into a dish, the frequency of chromosome mis-segregation drastically increased. The cells that were less tied to structures in their tissue were not affected by the lack of architecture in culture dishes.

The researchers found that maintaining the architectural conditions of the cell’s native environment is essential for chromosome stability. Cells removed from the context of their tissue don’t always faithfully represent natural processes.

The researchers determined that architecture didn’t have an obvious effect on the expression of known genes involved in segregation. The disruption in tissue architecture likely causes mechanical changes that disrupt segregation, in a manner that is independent of mutations or gene expression changes.

“It was surprising to us that for something so intrinsic to the cell — something that's happening entirely within the cell and so fundamental to the cell's existence — where that cell is sitting actually matters quite a bit,” Knouse says.

Through the Cancer Genome Project, scientists learned that despite high rates of chromosome mis-segregation, many cancers lack any mutations to the cellular machinery that controls chromosome partitioning. This left scientists searching for the cause of the increase of these division errors. This study suggests that tissue architecture could be the culprit.

Cancer development often involves disruption of tissue architecture, whether during tumor growth or metastasis. This disruption of the extracellular environment could trigger chromosome segregation errors in the cells within the tumor.

“I think [this paper] really could be the explanation for why certain kinds of cancers become chromosomally unstable,” says Iain Cheeseman, a professor of biology at MIT and a member of the Whitehead Institute, who was not involved in the study.

The results point not only to a new understanding of the cellular mechanical triggers and effects of cancers, but also to a new understanding of how cell biology must be studied.

“Clearly a two-dimensional culture system does not faithfully recapitulate even the most fundamental processes, like chromosome segregation,” Knouse says. “As cell biologists we really must start recognizing that context matters.”

This work was supported by the National Institutes of Health, the Kathy and Curt Marble Cancer Research Fund, and the Koch Institute Support (core) Grant from the National Cancer Institute.

Pushing the plasma density limit

For decades, researchers have been exploring ways to replicate on Earth the physical process of fusion that occurs naturally in the sun and other stars. Confined by its own strong gravitational field, the sun’s burning plasma is a sphere of fusing particles, producing the heat and light that makes life possible on earth. But the path to a creating a commercially viable fusion reactor, which would provide the world with a virtually endless source of clean energy, is filled with challenges.

Researchers have focused on the tokamak, a device that heats and confines turbulent plasma fuel in a donut-shaped chamber long enough to create fusion. Because plasma responds to magnetic fields, the torus is wrapped in magnets, which guide the fusing plasma particles around the toroidal chamber and away from the walls. Tokamaks have been able to sustain these reactions only in short pulses. To be a practical source of energy, they will need to operate in a steady state, around the clock.

Researchers at MIT’s Plasma Science and Fusion Center (PSFC) have now demonstrated how microwaves can be used to overcome barriers to steady-state tokamak operation. In experiments performed on MIT’s Alcator C-Mod tokamak before it ended operation in September 2016, research scientist Seung Gyou Baek and his colleagues studied a method of driving current to heat the plasma called Lower Hybrid Current Drive (LHCD). The technique generates plasma current by launching microwaves into the tokamak, pushing the electrons in one direction — a prerequisite for steady-state operation.

Furthermore, the strength of the Alcator magnets has allowed researchers to investigate LHCD at a plasma density high enough to be relevant for a fusion reactor. The encouraging results of their experiments have been published in Physical Review Letters.

Pioneering LHCD

“The conventional way of running a tokamak uses a central solenoid to drive the current inductively,” Baek says, referring to the magnetic coil that fills the center of the torus. “But that inherently restricts the duration of the tokamak pulse, which in turn limits the ability to scale the tokamak into a steady-state power reactor.”

Baek and his colleagues believe LHCD is the solution to this problem.

MIT scientists have pioneered LHCD since the 1970s, using a series of “Alcator” tokamaks known for their compact size and high magnetic fields. On Alcator C-Mod, LHCD was found to be efficient for driving currents at low density, demonstrating plasma current could be sustained non-inductively. However, researchers discovered that as they raised the density in these experiments to the higher levels necessary for steady-state operation, the effectiveness of LHCD to generate plasma current disappeared.

This fall-off in effectiveness as density increased was first studied on Alcator C-Mod by research scientist Gregory Wallace.

“He measured the fall-off to be much faster than expected, which was not predicted by theory,” Baek explains. “The last decade people have been trying to understand this, because unless this problem is solved you can’t really use this in a reactor.”

Researchers needed to find a way to boost effectiveness and overcome the LHCD density limit. Finding the answer would require a close examination of how lower hybrid (LH) waves respond to the tokamak environment.

Driving the current

Lower hybrid waves drive plasma current by transferring their momentum and energy to electrons in the plasma.

Head of the PSFC’s Physics Theory and Computation Division, senior research scientist Paul Bonoli compares the process to surfing.

“You are on a surf board and you have a wave come by. If you just sit there the wave will kind of go by you,” Bonoli says. “But if you start paddling, and you get near the same speed as the wave, the wave picks you up and starts transferring energy to the surf board. Well, if you inject radio waves, like LH waves, that are moving at velocities near the speed of the particles in the plasma, the waves start to give up their energy to these particles.”

Temperatures in today’s tokamaks — including C-Mod — are not high enough to provide good matching conditions for the wave to transfer all its momentum to the plasma particles on the first pass from the antenna, which launches the waves to the core plasma. Consequently, researchers noticed, the injected microwave travels through the core of the plasma and beyond, eventually interacting multiple times with the edge, where its power dissipates, particularly when the density is high.

Exploring the scrape-off layer

Baek describes this edge as a boundary area outside the main core of the plasma where, in order to control the plasma, researchers can drain — or “scrape-off” — heat, particles, and impurities through a divertor. This edge has turbulence, which, at higher densities, interacts with the injected microwaves, scattering them, and dissipating their energy.

“The scrape-off layer is a very thin region. In the past RF scientists didn’t really pay attention to it,” Baek says. “Our experiments have shown in the last several years that interaction there can be really important in understanding the problem, and by controlling it properly you can overcome the density limit problem.”

Baek credits extensive simulations by Wallace and PSFC research scientist Syun’ichi Shiraiwa for indicating that the scrape-off layer was most likely the location where LH wave power was being lost.

Detailed research on the edge and scrape-off-layer conducted on Alcator C-Mod in the last two decades has documented that raising the total electrical current in the plasma narrows the width of the scrape-off-layer and reduces the level of turbulence there, suggesting that it may reduce or eliminate its deleterious effects on the microwaves.

Motivated by this, PSFC researchers devised an LHCD experiment to push the total current by from 500,000 Amps to 1,400,000 Amps, enabled by C-Mod’s high-field tokamak operation. They found that the effectiveness of LCHD to generate plasma current, which had been lost at high density, reappeared. Making the width of the turbulent scrape-off layer very narrow prevents it from dissipating the microwaves, allowing higher densities to be reached beyond the LHCD density limit.

The results from these experiments suggest a path to a steady-state fusion reactor. Baek believes they also provide additional experimental support to proposals by the PSFC to place the LHCD antenna at the high-field (inboard) side of a tokamak, near the central solenoid. Research suggests that placing it in this quiet area, as opposed to the turbulent outer midplane, would minimize destructive wave interactions in the plasma edge, while protecting the antenna and increasing its effectiveness. Principal Research scientist Steven Wukitch is currently pursuing new LHCD research in this area through PSFCs’ collaboration with the DIII-D tokamak in San Diego.

Although existing tokamaks with LHCD are not operating at the high densities of C-Mod, Baek feels that the relationship between the current drive and the scrape-off layer could be investigated on any tokamak.

“I hope our recipe for improving LHCD performance will be explored on other machines, and that these results invigorate further research toward steady-state tokamak operation,” he says.