SKI Study Sheds Light on How a Natural Defense Against Viruses Can Lead to Mutations in Cancer Cells

The body deploys many weapons to defend against internal and external threats. One tactic used by cells involves a group of proteins called APOBEC3 enzymes. These enzymes can disable viruses by disrupting the invaders’ genetic material. They also protect against certain genetic mistakes that develop within a cell’s own genome. However, APOBEC3 enzymes sometimes misfire and mutate a cell’s own DNA.

Researchers had noticed that the patterns of mutations that APOBEC3 enzymes cause in viruses looked familiar — they also show up in the cells of about half of all cancers, especially breast and bladder tumors. What’s more, high levels of these enzymes in the cancer cells have been associated with poor prognosis (outcome), both in animal models and people. This suggested that APOBEC3 might be contributing to mutations in cancer, but there was no solid proof.

Now a research team led by Sloan Kettering Institute (SKI) molecular biologist John Maciejowski has found strong evidence that APOBEC3 enzymes play a role in causing the cancer-related mutations. The team also was able to identify which specific APOBEC3 enzyme type — APOBEC3A — is most responsible for triggering the mutations found in cancer cells.

“We now know APOBEC3 enzymes are involved, and we have narrowed down which enzyme to focus on further to try to understand how it gives rise to mutations in cancer,” Dr. Maciejowski says. “It seems likely that contributing to these mutations makes APOBEC3A an important player in driving cancer development, although that is still an area of active investigation.”

The team published their results online on July 20, 2022, in Nature.

A Better Research Model To Study APOBEC3

Scientists had struggled to clarify the connection between APOBEC3 and cancer because they did not have adequate models. Although researchers could trigger cancer in mice by artificially boosting APOBEC3 levels, it was not clear whether this occurred endogenously — originating naturally within the body. And mice have only one APOBEC3-producing gene, not seven as humans do, so a discovery in rodents might not hold true in people.

“The APOBEC3 enzymes as we know them really appear only in primates,” Dr. Maciejowski says. “They came along late in the evolutionary process.”

In recent years, a better tool emerged. Mia Petljak, a researcher at the Broad Institute of MIT and Harvard, had grown various human cancer cell lines in a lab dish. She performed whole-genome sequencing of the cells twice, about 100 days apart. This allowed her to infer which mutations occurred during that period.

Dr. Maciejowski’s team was eager to use this experimental system to investigate APOBEC3, so they collaborated with Dr. Petljak to study the cancer cells. (Dr. Petljak is a co-corresponding author on the Nature paper.)

“We thought this could help us finally find the smoking gun showing that an endogenous APOBEC3 enzyme can produce these mutations,” he says.

The researchers performed classic loss-of-function experiments: They would knock out specific APOBEC3 genes one at a time at the beginning of the 100-day period to see what unfolded as the cells replicated.

The prevailing theory among scientists had been that APOBEC3B was the most likely of the seven enzymes to be driving the cancer. But the experiments showed that loss of APOBEC3B function did not have much impact on the mutations — they still occurred. However, knocking out the gene for APOBEC3A resulted in very few mutations. This suggests APOBEC3A is likely the main driver of the cancer-related mutations.

“Right now, it looks like A is more relevant than B,” Dr. Maciejowski says. “When we knocked out A and B both, the mutation number was even smaller, so B might contribute as well, but to a lesser degree.”

APOBEC3A Mutations Fade In and Out

Drs. Maciejowski and Petljak will continue their ongoing collaboration by focusing on APOBEC3A-related mutations to better understand their pattern and how they potentially contribute to the development of cancer. Right now, it appears very complex: The APOBEC3 mutations seem to occur only in some cells — even those in the same cell line — and in short spurts.

“It looks like the effect may occur at high levels, but in a small subset of cells,” Dr. Maciejowski says. “It flicks on, causes a mutation burst, and then turns off. It could be shuffling the genetic deck in a way that helps the tumor survive any negative external forces, whether it’s the immune system or therapeutic interventions. We’re now trying to understand the mechanistic basis for these kinds of mutational episodes.”

They also are trying to understand what triggers APOBEC3A dysfunction in the first place. “This enzyme should normally not be expressed in these cell types, and yet it’s getting turned on,” he says. “Something is triggering the aberrant APOBEC3 response. We hope to now use our cancer cell line models to identify these triggers.”