Today’s cancer therapies have some painful side effects, and scientists are on the hunt for better treatments. Chemotherapy is the major cancer treatment used today, and it works by stopping cell division — all of it. Although cancer cells take the hardest hit (they have very rapid division rates), healthy cells are still affected. This results in those dreaded side effects, including hair loss, easy bruising, nausea, mouth and throat problems, fertility problems, and more.

Cells are good at dividing so that they can make copies of themselves, and most of the time, they are also good at recognizing when they need to stop. When cells become cancerous, they divide, and continue dividing, and the cancer spreads. This abnormal cell division is usually caused by mutations in the cell’s DNA. This is often triggered by DNA damage, for example from UV exposure (as in the skin) or toxins in tobacco smoke (as in the lungs). 

UV rays from the sun can damage DNA and lead to cancer. Image Credit: Getty Images / Joel Carillet

There are other drugs that stop cell division, however. To learn more about them, I spoke with Dr. Chen Yang, a postdoc in Sabrina Spencer’s lab at the University of Colorado Boulder. Yang and colleagues took a look at a class of drugs called BRAF inhibitors. One of the places DNA mutations can occur that results in cancer is the BRAF gene. Mutating BRAF activates unhindered cell division. BRAF inhibitors suppress the BRAF gene (and the mutated BRAF as well), so they can stop the mutation from causing cancer. They are thought to have very few side effects compared to chemotherapy, and they fight cancer just fine – mostly. In some patients, relapse occurs after 6-12 months of treatment, when some cells go back to being cancerous. The Spencer lab wanted to find out why that happens. By identifying the many ways cancer cells can become cancerous and evade treatment, Yang and colleagues hope to gain an increased understanding of this complicated system, and pave the way for improved treatments in the future.

In their most recent work, they figured out how cells resist anti-cancer drugs like BRAF inhibitors. Usually, a BRAF inhibiting drug commands the mutated BRAF to stop driving cell division. And while most of the cells behave properly after that, a few cells might escape the inhibition and go back to being cancerous. After an appearance of remission, these “escapee” cells go back to dividing again, and prior to Yang’s research, we had no idea how. This evaluation of escapees and non-escapees is the main topic of Yang’s recent Nature Communications paper.

To conduct such a study, Yang had to be able to tell escapees and healthy cells apart. Cells pass through phases of division and rest, and their internal chemistry can indicate which phase they are in. She attached colorful stains to the chemicals inside of a cell to use them as indicators for who is dividing and who isn’t. From there, she added a BRAF inhibitor and then looked for escapees. 

Now, there were two hypotheses as to how these escapees were escaping. Perhaps there is a DNA mutation for escape already lurking in the background. In such a case, when Yang adds a BRAF inhibitor, only healthy cells will stop dividing, and the mutants will take over. But it’s also possible that the escapees weren’t cancerous (or potentially cancerous) to begin with. Instead, some of the normal cells might change after treatment. Yang wanted to know: are escapees already mutated, allowing them to beat the BRAF inhibitors? Or do they turn to the dark side after they are exposed to drugs? 

Escapee cells (turquoise) and non-escapee cells (blue) after being treated with BRAF inhibitor. Image from Yang’s article.

To test this, Yang showered the cells in BRAF inhibitors, waited for escapees to show up, sorted non-escapees from escapees, and let each group grow up living a drug-free life. After this drug break, she added BRAF inhibitors again. If escapees were born this way, they would already be mutants, and they would grow faster than they did before because they would no longer be in the minority. If escapees were normal cells that turn after drug exposure, then they would forget their escape mechanism after their little BRAF inhibitor-free holiday. In this case, they would look like the beginning population again, and show the same initial slow growth after being given the BRAF inhibitor. They would have to re-learn their escape strategy.

In Yang’s study, cell population growth rates were the same for first and second BRAF inhibitor treatment. That was conclusive evidence: the cells all start out normal, but some turn to the dark side, becoming cancerous after drug exposure. That’s a great first step toward a more complete understanding of why cancer relapse is seen in some patients treated with BRAF inhibitors. Their cancer cells initially respond well to the treatment, but some eventually find a way to rebel and turn cancerous. The next step is to figure out what that rebellion strategy is.

Cells have lots of genes, and they can’t use them all at the same time. Instead, they turn genes on and off to focus on what they need at any moment. So Yang wanted to know, what if she tracked all the genes as they turn on and off in the cell, comparing active genes between escapees and non-escapees? She could then see if escapees are using genes that non-escapees are silencing, or vice versa. In the same way that construction workers take copies of blueprints and use them to build houses, cells make copies of DNA in the form of mRNA, and use the mRNA blueprint to build proteins. These proteins are the workers inside the cell, carrying out jobs including cell division. That means that while DNA represents all the information, mRNA represents all information that the cell is currently using. Instead of a “blueprint”, each mRNA is called a transcript. The number of mRNA transcripts present for particular genes can tell us which genes are turned on in the cell.

After looking at no fewer than 400,000 transcripts per cell, Yang and colleagues found 40 genes uniquely expressed in escapees. If they’re only expressed in escapee cells, they’re probably contributing to escape. In theory, each escapee could be using a different combination of these 40 genes. That implies that a tumor is not a blob of identical cells, each one disobeying in the same way. No, a tumor is a madhouse with different escape mechanisms activated in each cell! There are common genes related to cell division (including BRAF), but each cell is mostly coming up with its own rebellion strategy, with a unique combination of those 40 genes giving it the ability to escape. 

One of these genes, for example, is turned on in response to stress. Cells can get stressed when something forces the cell to work unusually hard to maintain normal living conditions, such as DNA damage. Since the Top 40 list identified by Yang includes stress response genes, it’s possible that DNA damage from BRAF inhibitors is triggering stress, and in turn, triggering cancer relapse. While it’s discouraging to think these BRAF inhibitors are not as safe as we previously thought, this information can help scientists develop better, safer treatments in the future. The first step is understanding how current treatments can go wrong.

Yang’s model for how escapees become drug resistant. Image from Yang’s article.

There is much to be done in the fight against cancer, but research like this empowers innovation towards new treatments. If we peer into the inner workings of a cancer cell, the way Yang and colleagues have, we can learn to hack the system and fight back. 


Special thanks to Dr. Chen Yang for her support in the making of this article. Extended thanks to the Spencer lab for all their work on this awesome project!  

By Hannah Edstrom

Posted by Science Buffs

A CU Boulder STEM Blog

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