Scientists first noticed the phenomenon when examining cancer cells under a microscope in the early 1900s. They observed that, as cancer cells multiplied, some ended up with too many chromosomes, structures that we now know carry genes. Others wound up with too few.

The jarring observation led a German embryologist to propose that aberrant numbers of chromosomes weren’t just a hallmark of cancer — perhaps they were causing it. The idea largely fell out of favor as scientists began to discover dozens of individual genes that caused cancer and developed drugs to target them.

But cancer cells’ chromosomal disorder remained an in-your-face oddity — a common thread in 90 percent of cancers. Everyone knew it was there; no one was sure why or what it meant.

“It was indeed overlooked to some extent, and the reason for that is it was just really challenging to study,” said Uri Ben-David, an associate professor of human molecular genetics and biochemistry at Tel Aviv University who was not involved in the new study. “For many decades, it was kind of ignored. It was like an elephant in the cancer research room.”

In the new study, scientists have figured out how to tackle the mystery using a clever CRISPR hack. Their work showed that without extra chromosomes, certain cancer cells can no longer seed tumors in animals.

Cancer driver or downstream effect?

Humans have 23 pairs of chromosomes, long threadlike structures made up of DNA and protein that carry our genes. Normally when cells divide, chromosomes make copies of themselves and then separate tidily and symmetrically into new cells. But in cancer, this choreography goes helter-skelter, and cells end up with abnormal numbers of chromosomes.

For decades, a classic conundrum in science stymied research into this phenomenon: Were the aberrations the cause of cancer, or simply a sign that things had already gone haywire in the cell? Back then, chromosomes weren’t easy to add or remove, so scientists searching for answers had to rely largely on intriguing correlations.

One study exposed melanoma cells to a chemical that further disrupted their chromosomes; those cells were faster to develop resistance to a targeted drug, suggesting that chromosomal abnormalities might play a role in cancer’s ability to thwart drugs. Another study found that the more chromosomally unstable a patient’s tumor cells were, the more likely their cancer was aggressive and their prognosis poor.

Again, the question of cause and effect loomed: Could it be that chromosomal disruption was playing a role in those cancers, or was it only a downstream effect?

With the invention of CRISPR gene editing technology a decade ago, scientists gained the ability to add, delete or tweak genes. But deleting a whole chromosome is a different matter.

To do full-scale chromosome engineering, Jason Sheltzer, a cancer biologist at Yale School of Medicine, and his team had to deploy a CRISPR hack. First, they inserted a gene from the herpes virus onto a cancer cell’s extra chromosomes. Initially, they chose chromosome 1q, which is one of the first to gain or lose extra copies during the development of breast cancer.

They then used a herpes treatment, ganciclovir, to target the modified chromosomes. The technique killed the cells with extra copies, leaving behind cancer cells with normal numbers of chromosomes.

When they tried to grow tumors from this subpopulation of cancer cells, they found that the cells were no longer capable of seeding tumors in a petri dish or in live mice. To Sheltzer, this was clear evidence that extra chromosomes weren’t just an effect, but a driver of the disease.

“It has a central role,” Sheltzer said.

New ways to attack cancer

For now, the technique is a tool, not a therapy. It’s not yet feasible to think about restoring normal numbers of chromosomes in cancer cells as a way of staving off the disease.

But it may point toward a different way to target cancer in the future. Genetic understanding of cancer has led to therapies that target specific mutations that drive its progression. But cancer is a wily foe and often develops resistance to any one therapeutic approach.

The recognition that extra chromosomes are crucial to driving cancer means researchers can attack from a new direction: finding and killing cells that contain extra chromosomes.

Because chromosomes contain hundreds or thousands of genes, such an approach could expand the number of targets. Even if the cancer eventually became “resistant” to such a drug by losing its extra chromosomes, the study suggests that doing so might also squash its cancer-causing ability.

In essence, the extra chromosome becomes a new therapeutic vulnerability, Sheltzer said. Because the cells have all this other genetic material, such cells may “become sensitive to drugs targeting a gene, even if it has nothing to do with cancer.”