Courtesy of Diego Dibitetto/Smolka Lab

October 12, 2022

Cornell Researchers Discover a New Mechanism of Cancer Chemotherapy Resistance

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The Smolka Lab, led by Prof. Marcus Smolka, molecular biology and genetics, recently published a study shedding light on a novel pathway that explains how cancer cells can become resistant to chemotherapy and offering a promising mechanism to prevent chemo-resistance —the process by which cancer cells become tolerant to chemotherapeutic drugs.

Researchers found that chemo-resistance originates from the process of DNA replication. During replication, DNA separates into individual strands so that each strand can be copied to create two new double helices. The region where the separation and copying of DNA occurs is called a replication fork.

Chemotherapeutic drugs work by creating blocks on the DNA of cells as they replicate. Cells can avoid collisions with these blocks and protect their DNA by slowing down replication forks.

“Slowing down the fork gives time to remove the obstacles so the cell can replicate. As a fork moves forward, it senses that there is an obstacle and reverts back,” Smolka said. “Not much is known about how cancer cells can actually acquire this capacity to slow down forks. That’s where our work gets into trying to understand the early signals that mediate fork reversal.”

The Smolka Lab was uniquely positioned to study the early processes of fork reversal with over two decades of experience studying kinases — proteins that regulate pathways of cellular response. For this study, the researchers focused on a specific kinase involved in protecting the integrity of the genome: DNA-PKcs.

“For the past 20 years, most of the work around DNA-PKcs has been about how it is involved in the repair of DNA double strand breaks,” said Shannon Marshall, a graduate student in the Smolka Lab.“Now our lab and others have found this really interesting phenomenon. DNA-PKcs, which is typically thought to only be recruited to sites of DNA breaks, is also present at ongoing replication forks. We see this as normal replication is occurring, indicating the DNA-PKcs is moving along with replication forks. That made us wonder if this protein is somehow involved in regulating responses to replication stress.”

To test their hypothesis, the researchers used DNA fiber assays with fluorescent colors to detect the movement of replication forks under active and inactive DNA-PKcs. They confirmed that active DNA-PKcs promotes fork reversal. In fork reversal, replication forks switch their direction of movement upon encountering stress.

“We found that DNA-PKcs regulates the speed of the replication fork. If you inhibit this kinase, the forks cannot slow down anymore,” Smolka said.

The researchers applied these findings in a model of BRCA2 deficient breast cancer to better understand the translational implications for cancer therapeutics. Currently, inhibitors of DNA-PKcs are used in clinical trials in tandem with radiotherapy to induce DNA damage that destroys cancer cells. The team’s discovery offers an entirely different mechanism to more effectively target treatment-resistant cells.

“We were able to use a model for BRCA2 deficient cancer cells that use this fork reversal process as a mechanism for chemo-resistance. In these cells, we showed that inhibiting the kinase DNA-PKcs actually re-sensitizes them to the chemotherapeutic drug,” Marshall said. “This mechanism is a way through which we can re-sensitize cancer cells and address chemo-resistance.”

From a research perspective, this work opens the door to new directions in understanding the mechanisms of how DNA-PKcs exerts its effects.

“How does DNA-PKcs sense obstacles in DNA replication? What proteins is DNA-PKcs affecting? If we can address these two questions, we can find other proteins that are involved in the decision making processes and manipulate tolerance in different ways,” Smolka said. “We have developed technologies that we can screen for targets of this kinase, and we are testing a new target now that could explain how DNA-PKcs slows down the forks.”

For Marshall, this research is inspiring and meaningful because of its potential clinical impact.
“In this project, we were able to work on a translational aspect of research where we could hopefully, in the next couple of years, begin to see implementation in cancer treatments, at least in terms of clinical trials. That’s really the part that meant a lot to me,” Marshall said.

Reflecting back on his own career and research process, Smolka encourages students to enjoy their studies and nurture a genuine curiosity in science.

“This [research] highlights the importance of basic science as the conduit to allow all of this research to happen and eventually lead to discoveries that can be applied,” Smolka said. “A major driver of these discoveries is really the curiosity in fundamental biology and the pursuit of basic questions.”