Some breast cancer types are more likely than others to recur. Researchers have known this for more than a decade.

But they have long wondered why.

“How did those tumor types arise?” said Christina Curtis, PhD, a professor of medicine, genetics and biomedical data science at Stanford University, Stanford, California. “They’re all breast cancers. They’re all estrogen receptor–positive. But these groups are different. When did they become different, and how is that determined?”

Curtis and her colleagues are finally starting to answer these questions. They recently broke new ground in a study linking differences in cancer-related genes to disease subtype and aggressiveness.

Curtis and her colleagues found that, like fingers molding clay, the genes you’re born with can coax the immune system into shape. DNA inherited from our parents is known as the germline genome. It affects whether the immune system attacks or retreats when confronted with variations that may lead to breast cancer.

“It turns out, the germline genome sculpts tumor evolution,” said Curtis.

The study is part of a growing effort to understand “precancer” — the critical period after cells have started to grow abnormally but before they’ve developed into cancer — a research trend that could trigger a decisive shift in how cancer treatments are realized. Therapeutics could be designed on the basis of the biology of these precancerous cells.

While biotech start-ups push new tests to catch cancer early, researchers like Curtis hope to stop cancer before it even starts.

“This is a really exciting area of research,” said Susan Domchek, MD, executive director of the Basser Center for BRCA at the University of Pennsylvania, Philadelphia, who was not involved in the study. “What we hope for is that, over time, we’re going to have more and more biologically driven interception.”

‘We’re Basically Unearthing the Dark Matter of the Human Genome’

Of course, we already have mechanical ways of heading off cancer, like having a precancerous polyp removed. But for the Stanford researchers, biologic interception is the goal. They hope to figure out how to use the immune system to stop the cancer.

In their study, they looked at DNA variabilities known as somatic aberrations or single-nucleotide protein sequences (SNPs). The HER2 gene, for example, can contain SNPs — possibly affecting how the HER2 protein regulates breast cell growth and division.

“There’s been a huge effort through genome-wide association studies to link SNPs to cancer outcomes and risk,” Curtis said.

Focusing on people with a genetic predisposition for breast cancer, Curtis used machine learning to show that these variabilities can occur in specific epitopes (protein features that can trigger an immune response).

They also found that heightened variability can show up in a region of the genome called the human leukocyte antigen (HLA). Each HLA molecule can contain many epitopes.

“We developed a whole new algorithm to compute this ‘germline epitope burden’,” Curtis said. “We’re basically unearthing the dark matter of the human genome to ask about the interplay between SNPs and HLA class one presentation.”

These aberration-rich regions can grab the immune system’s attention. Sometimes the immune system identifies and eradicates those epitopes.

In that case: “I have immunosurveillance. I’ve cured my cancer,” said Nora Disis, PhD, director of the Cancer Vaccine Institute and a professor of medicine at the University of Washington, Seattle. Disis was not involved in the study.

But other times, the immune system finds a way around the high “epitope burden,” and the tumors become more aggressive and immunosuppressive. That’s when cancer forms.

This suggests a “critical juncture between preinvasive and invasive disease,” Curtis said.

And that “critical juncture” may very well be the optimal time for intervention.

The Precancer Push

Stanford’s findings add information to prior biomarkers and may provide a way to identify “bad acting tumors” from a simple blood draw measuring germline epitope burden, Curtis said. Looking further ahead, she added, “This also reveals a new source of epitopes that might be immunogenic and might be informative for the development of vaccines.”

Many labs are trying to understand the biology of precancer and exploring possible vaccines.

The National Cancer Institute’s Human Tumor Atlas Network is building three-dimensional models of the evolution from precancerous to advanced disease. And researchers at the Cancer Vaccine Institute at the University of Washington are developing a vaccine for a precancerous lesion linked to many ovarian cancers.

Domchek’s research explores whether breast cancers caused by mutations in the BRCA 1 and 2 genes can be intercepted at very early stages. In a clinical trial of healthy people with those mutations, Domchek and her colleagues are attempting to “rev up the immune system to tackle telomerase,” an enzyme that’s over-expressed in 95% of cancers. The hope is for this experimental vaccine to lower their risk of developing cancer.

At the Fred Hutch Cancer Center, Seattle, Ming Yu, PhD, is studying how senescent cells affect immune cells in precancer. As cells age and stop dividing, she said, they can accumulate and create a “tumor-promoting microenvironment” in older people.

Yu has found that the antiaging drug rapamycin can eliminate those “zombie cells” in mice. She’s studying whether the “cleanup” can help prevent cancer and expects results in a few months.

In the years and decades to come, all of this could lead to a new era in cancer treatment.

“Most drug development starts with people with advanced cancer and then goes into the earlier and earlier spaces,” said Domchek. “But it may be that we’re thinking about it all wrong and that you really have to understand the unique biology of early lesions to go after them.”