A Stanford Medicine study of thousands of breast cancers has found that inherited gene sequences may be powerful predictors of the breast cancer type that might develop decades later, and how deadly that cancer might be. The study offers up new insights into the interplay between newly arisen cancer cells and the immune system and may help researchers and clinicians better predict and combat breast tumors.

The findings challenge the notion that most cancers arise as the result of random mutations that accumulate during our lifetimes. Instead, they point to the active involvement of gene sequences inherited from our parents—our germline genome—in determining whether cells bearing potential cancer-causing mutations are recognized and eliminated by the immune system or whether they can remain undetected, to become nascent cancers. The results could lead to the development of biomarkers that predict the risk of invasive breast cancer recurrence and risk stratification within relevant breast cancer subtypes.

“Apart from a few highly penetrant genes that confer significant cancer risk, the role of heredity factors remains poorly understood, and most malignancies are assumed to result from random errors during cell division or bad luck,” said Christina Curtis, PhD, the RZ Cao Professor of Medicine and a professor of genetics and biomedical data science. “This would imply that tumor initiation is random, but that is not what we observe. Rather, we find that the path to tumor development is constrained by hereditary factors and immunity. This new result unearths a new class of biomarkers to forecast tumor progression and an entirely new way of understanding breast cancer origins.”

Senior study author Curtis, together with postdoctoral scholar and lead author Kathleen Houlahan, PhD, and colleagues, reported on their findings in Science, in a paper titled “Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity.” In their research summary, the investigators concluded, “These data indicate that supposedly ‘benign’ germline variants with little to no functional genic effect may, in aggregate, sculpt breast cancer subtypes and disease aggression through immunoediting … Exploiting germline-mediated immunoediting may inform the development of biomarkers that predict risk of invasive breast cancer recurrence and further refine risk stratification within invasive breast cancer subtypes.”

Cancer is defined by a set of abnormal biological capacities, known as “hallmarks of cancer,” which can be acquired by hijacking various cellular processes, the authors explained. “Decades of histopathologic assessment and molecular profiling of human tumors have demonstrated that there are multiple ways cells can acquire each hallmark.” This means that tumors with the same clinical characteristics can vary dramatically across individuals, and the distinct molecular vulnerabilities can have important prognostic and therapeutic implications. However, the team noted, “It is unclear when these differences originate.”

The genes we inherit from our parents are known as our germline genome. They’re mirrors of our parents’ genetic makeup, and they can vary among people in small ways that give some of us blue eyes, brown hair, or type O blood. Oncogenic aberrations are also acquired within the context of germline genomes, which differ across individuals at millions of polymorphic sites, the investigators noted, but how germline DNA variation impacts cancer development isn’t clear. “It remains poorly understood how inherited variants impact the evolution of a tumor,” they stated.

In contrast, most cancer-associated genes are part of what’s known as our somatic genome. As we live our lives, our cells divide and die in the tens of millions. Each time the DNA in a cell is copied, mistakes happen and mutations can accumulate. DNA in tumors is often compared with the germline genomes in blood or normal tissues in an individual to pinpoint which changes likely led to the cell’s cancerous transformation.

Currently, only a few high-profile cancer-associated mutations in genes are regularly used to predict cancers. Those include BRCA1 and BRCA2, which occur in about one of every 500 women and confer an increased risk of breast or ovarian cancer, and rarer mutations in a gene called TP53 that causes a disease called Li Fraumeni syndrome, which predisposes to childhood and adult-onset tumors. “… deleterious germline variants in BRCA1 and, to a lesser extent, BRCA2, are preferentially associated with the development of triple negative breast cancer and estrogen receptor (ER)–positive (ER+) breast cancer, respectively, implying that germline variants modulate specific subtypes of disease,” the team continued. Other than BRCA1, BRCA2, and TP53, identifying other germline mutations strongly associated with future cancers has proven difficult.

In 2012, Curtis began a deep dive—assisted by machine learning—into the types of somatic mutations that occur in thousands of breast cancers. She was eventually able to categorize the disease into 11 subtypes with varying prognoses and risk of recurrence, finding that four of the 11 groups were significantly more likely to recur even 10 or 20 years after diagnosis—critical information for clinicians making treatment decisions and discussing long-term prognoses with their patients.

Prior studies have shown that people with inherited BRCA1 or BRCA2 mutations tend to develop a subtype of breast cancer known as triple negative breast cancer. This correlation implies some impact of the germline genome that affects what subtype of breast cancer someone might develop. “We wanted to understand how inherited DNA might sculpt how a tumor evolves,” Houlahan said.

To do so, they took a close look at the immune system. The outer membranes of cells routinely display small chunks of proteins found in their cytoplasm. The foundations for this display are what are known as HLA proteins, and they are highly variable among individuals. The immune system’s T cells recognize epitopes that might signal something is amiss inside the cell. A cell infected with a virus, for example, will display bits of viral proteins while a sick or cancerous cell will display abnormal proteins. These abnormal signals trigger the T cells to destroy the offenders.

Houlahan and Curtis decided to focus on oncogenes, normal genes that, when mutated, can free a cell from regulatory pathways meant to keep it on the straight and narrow. Often, these mutations take the form of amplifications, when multiple copies of the normal gene are arranged nose to tail along the DNA. Amplifications in specific oncogenes drive different cancer pathways and were used to differentiate one breast cancer subtype from another in Curtis’ original studies.

The researchers wondered whether highly recognizable epitopes would be more likely to attract T cells’ attention than other, more modest displays. If so, a cell that had inherited a flashy version of an oncogene might be less able to pull off its amplification without alerting the immune system than a cell with a more modest version of the same gene.

For their newly reported research, the team studied nearly 6,000 breast tumors spanning various stages of disease to learn whether the subtype of each tumor correlated with the patients’ germline oncogene sequences. They found that people who had inherited an oncogene with a high germline-derived epitope burden (GEB) and an HLA type that can display that epitope prominently were significantly less likely to develop breast cancer subtypes in which that oncogene is amplified. “Interrogating 5,870 breast cancer lesions, we demonstrated that germline-derived epitopes in recurrently amplified genes influence somatic evolution by mediating immunoediting,” they wrote. “Individuals with a high germline-epitope burden in human epidermal growth factor receptor 2 (HER2/ERBB2) are less likely to develop HER2-positive breast cancer compared with other subtypes.”

There was a surprise, though. The researchers found that cancers with a large germline epitope burden that manage to escape immune cell recognition early in their development tended to be more aggressive and have a poorer prognosis than their more subdued peers. “Tumors that overcame immune-mediated negative selection were more aggressive and exhibited microenvironments depleted of lymphocytes,” the authors further noted.

“At the early, pre-invasive stage, a high germline epitope burden is protective against cancer,” Houlahan said. “But once it’s been forced to wrestle with the immune system and come up with mechanisms to overcome it, tumors with high germline epitope burden are more aggressive and prone to metastasis. The pattern flips during tumor progression.” Curtis further explained, “Basically, there is a tug of war between tumor and immune cells. In the preinvasive setting, the nascent tumor may initially be more susceptible to immune surveillance and destruction. Indeed, many tumors are likely eliminated in this manner and go unnoticed. However, the immune system does not always win. Some tumor cells may not be eliminated and those that persist develop ways to evade immune recognition and destruction. Our findings shed light on this opaque process and may inform the optimal timing of therapeutic intervention, as well as how to make an immunologically cold tumor become hot, rendering it more sensitive to therapy.”

The researchers envision a future when the germline genome is used to further stratify the 11 breast cancer subtypes identified by Curtis to guide treatment decisions and improve prognoses and monitoring for recurrence. The study’s findings may also give additional clues in the hunt for personalized cancer immunotherapies and may enable clinicians to one day predict a healthy person’s risk of cancer from a simple blood sample.

The data thus have important clinical implications, the investigators stated. “ … germline variants can be measured from blood and thus represent a low-cost, minimally invasive biomarker that is not sufficiently harnessed at present … GEB measured from blood may be exploited to further stratify risk of relapse within breast cancer subtypes and to identify tumors with high lymphocyte infiltration.”

“Back in 2015, we had posited that some tumors are ‘born to be bad’—meaning that their malignant and even metastatic potential is determined early in the disease course,” Curtis said. “We and others have since corroborated this finding across multiple tumors, but these findings cast a whole new light on just how early this happens.” Added Houlahan, “Our findings not only explain which subtype of breast cancer an individual is likely to develop. But they also hint at how aggressive and prone to metastasizing that subtype will be. Beyond that, we anticipate that these inherited variants may influence a person’s risk of developing breast cancer.”

“We started with a bold hypothesis,” Curtis continued. “The field had not thought about tumor origins and evolution in this way. We’re examining other cancers through this new lens of heredity and acquired factors and tumor-immune co-evolution.”

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