Can Chromosomal Instability Drive Epigenetic Alterations in Cancer Cells?

A graduate student’s curiosity has uncovered a previously unknown link between two important hallmarks of cancer: chromosomal instability and epigenetic alterations. The resulting study, which was recently published in Nature, not only opens a fertile new area of basic research, but also has implications for clinical care.

Chromosomal instability has to do with changes in the number of chromosomes each cancer cell carries. Epigenetic alterations change which genes get turned on or off in a cell, but without modifying the cell’s DNA code.

In his first year as a doctoral student in pharmacology at Weill Cornell Medicine, Albert Agustinus did a rotation in the lab of Samuel Bakhoum, MD, PhD, whose research group at Memorial Sloan Kettering (MSK) Cancer Center studies how chromosomal instability drives cancer. Agustinus is also co-mentored by epigenetics expert Yael David, PhD, whose lab at MSK Institute takes a chemical biology approach to study the epigenetic regulation of transcription.

Recently, Agustinus recounted his first big “aha” moment in the project, for which he also received a prestigious drug discovery fellowship from the PhRMA Foundation. He was sitting next to a lab mate and peering through the microscope. The cells he was looking at had abnormal little mini-nuclei scattered throughout the cell—a common consequence of chromosomal instability. And they had been set up with fluorescent markers that would show the presence of epigenetic modifications. “The micronuclei were glowing much brighter than the primary nucleus,” Agustinus says. “My lab mate said to me, ‘I’ve never seen you smile that wide before’.”

Chromosomes gone wild

Chromosomes are tightly packaged strands of DNA that carry our genetic information. Normally, each of our cells has 46 chromosomes—23 from each parent. When a cell divides to make a new copy of itself, all those chromosomes are supposed to end up in the new cell, but the process can go dreadfully awry in cancer cells.

“The big question that my lab is trying to answer is how chromosomal instability drives cancer evolution, progression, metastasis, and drug resistance,” says Bakhoum. “It’s a feature of cancer, especially advanced cancers, where the normal process of cell division goes haywire. Instead of 46 chromosomes, you can have a cell with 69 chromosomes right next to a cell with 80 chromosomes.”

The prevailing wisdom in the field has been that cancer cells increase their chance of survival by shuffling up their genetic material when they divide. This process increases the odds that some random changes will allow a cancerous daughter cell to withstand the assaults of the immune system and medical interventions. “This new research, however, suggests that’s only part of the story,” says Bakhoum.

That’s because you can have two cancer cells, each with the same number of extra copies of a given chromosome, but each has different genes that are turned off or on. This is due to additional epigenetic changes.

“Our work further suggests that you don’t actually need mutations in the genes that encode epigenetic-modifying enzymes for epigenetic abnormalities to happen. All you need is to have ongoing chromosomal instability,” says Bakhoum. “It’s an unexpected finding, but really important. And it also explains why we often find chromosomal instability and epigenetic abnormalities in advanced, drug-resistant cancers, even when there is no evidence of the types of mutations that we would expect to create epigenetic havoc.”

What do micronuclei have to do with cancer?

Small, extra nuclei in cells, known as micronuclei, are usually rare and quickly get eliminated by the cell’s natural repair mechanisms. But when there are several of them, it’s a signal that something has gone horribly wrong, as happens in cancer.

Like a cell’s primary nucleus, these micronuclei contain packages of genetic material. And when these micronuclei burst—which they frequently do—the researchers found that it causes more problems.

The research demonstrated that the sequestration of chromosomes into micronuclei disrupts the organization of chromatin—a complex of genetic components that get packaged into chromosomes during cell division. This leads to ongoing epigenetic dysregulation, which continues long after a micronucleus is reintegrated into a cell’s primary nucleus.

And the repeated formation and reincorporation of micronuclei over many cycles of cell division leads to the buildup of epigenetic changes. These, in turn, lead to greater and greater differences between individual cancer cells.

The more variation between individual cancer cells within the same tumor, the more likely it is that some of the cells will be resistant to whatever treatment they’d be subjected to—allowing them to survive and continue their runaway growth.

Analyzing epigenetic changes

To understand and quantify the epigenetic changes happening inside the cells, the researchers use a series of sophisticated experiments to isolate the micronuclei and examine changes occurring in them compared to the cells’ primary nuclei. This allowed them to see patterns of histone modification, which, in turn, change access to the underlying genes.

“This allowed us to ask some important questions, like do we actually get transcription of genes that are important in specific pathways?” says David. “And the answer is, yes.”

They also compared intact versus ruptured micronuclei, revealing an even greater level of changes in the ones that had burst open. “We also found there were a lot more accessible promoter regions in the micronuclei than in the primary nuclei,” she adds.

In one key experiment, the researchers forced a chromosome to go out into a micronucleus and then allowed it to get reintegrated into the primary nucleus. They compared this adventuresome chromosome to one that stayed put.

“Our model chromosome, which happened to be chromosome Y, showed substantial changes in its epigenetic landscape and accessibility of its DNA,” says David. “This has major implications because of the significant impact the journey of a chromosome into a micronucleus has on the epigenetic changes of the primary nucleus, which we know, play a role in tumor progression and evolution.”

David adds this work opened whole new avenues of study. “Now that we’ve demonstrated that chromosomal instability and epigenetic changes are closely linked, we can go deeper and ask questions about precisely how and why,” says David.

Clinical implications of findings

More than just shedding light on the changes happening inside cancer cells, the team notes that the research holds promise for treating patients as well. Epigenetic changes are a reversible form of gene regulation—and several classes of drugs have already been developed to work on them.

Chromosomal instability and the presence of micronuclei might be used as biomarkers to help identify which patients might be more likely to be helped by epigenetic modifying drugs, says Bakhoum. Additionally, the findings may pave the way for new therapeutic approaches.

“There’s a question of whether we should be treating chromosomally unstable cells with these epigenetic modifying therapies,” says David. “This research demonstrates epigenetic changes can occur without those mutations being present.” Moreover, the study also suggests that ongoing research into drugs to target chromosomal instability directly might benefit from being combined with efforts to suppress epigenetic alterations, adds Bakhoum.

Another potential avenue would be to explore ways of targeting the micronuclei to prevent them from rupturing, which the research showed was a big driver of epigenetic changes, notes David. “I think this is a great example of a fundamental, basic science research discovery that, over the next five years, will open multiple interesting avenues for exploration and potential translation to the clinical setting.” 

- This press release was originally published on the Memorial Sloan Kettering Cancer Center website