• Dana-Farber researchers have identified a key mechanism involving the KMT2C and KMT2D genes that drives breast cancer metastasis to the brain.
• The study highlights the role of the KDM6A protein in promoting this spread, particularly in patients with triple-negative breast cancer.
• This discovery opens the door to potential new treatments targeting KDM6A to prevent brain metastasis in these patients.

When breast cancer metastasizes, it often heads for the brain, where it can be exceptionally difficult to root out. The key to preventing the spread of the cancer, or thwarting it if it does reach the brain, is to understand the mechanism that turns stationary tumor cells into nomadic intruders. 

In a recent study, a team of Dana-Farber scientists uncovered one such mechanism, a pathway leading from two mutated genes to an overactive gene that spurs metastasis in patients with triple-negative breast cancer. The findings, published in Nature Cell Biology, suggest that a protein lying midway along this path may be an excellent target for drugs to block the cancer’s spread. 

“In about half of patients with metastatic triple-negative or HER2-positive breast cancer, the cancer has spread to the brain,” says Dana-Farber’s Kornelia Polyak, MD, PhD, senior author of the study. “Compared to those whose cancer has spread to other sites, patients with brain metastases have the shortest overall survival. The need for better treatments for this group, particularly those with triple-negative cancer, is critical.” 

The study grew out of a piece of circumstantial evidence. Researchers knew that the genes KMT2C and KMT2D, which are often mutated in triple-negative breast cancer, are especially likely to be mutated in metastatic growths outside the breast. That suggests the mutations aren’t there by chance but play a role in the cancer’s spread. The nature of that role, however, was unclear. 

To find out, Marco Seehawer, PhD, a postdoctoral fellow in Polyak’s lab, took samples of non-metastatic triple-negative breast cancer cells from mice and used an RNA guide to shut down the KMT2C and KMT2D genes, basically duplicating what happens when the genes are mutated. He then injected the cells into mammary tissue of a group of female mice. Another group of mice received breast cancer cells with normal KMT2C and D. 

“We found that the growth of primary breast tumors – those that formed in the breast itself – was about the same in both sets of animals,” Polyak recounts. “But the mice that received cells with ‘knocked out’ [shut down] KMT2C and D had many more metastases in the liver, lungs, bones, and, especially, the brain.” 

The researchers performed an array of follow-up experiments to confirm that the loss of working KMT2C and D genes contributes to brain metastasis in mouse models, mirroring what happens in human patients. They then sought to trace the steps by which this takes place. 

The first clue was that KMT2C and KMT2D, the proteins made from the KMT2C and KMT2D genes, are known to exert a powerful influence on the activity of key genes. They do this by attaching methyl groups – packets of three hydrogen atoms surrounding a carbon atom – to proteins called histones, which hold DNA in place. This tends to loosen specific coils of DNA, altering the activity of genes in that region. 

Advanced technology enables scientists to map the precise locations of methyl groups and other “histone markers” across the genome. By comparing the number and locations of such markers in different sets of cells, researchers can spot differences in gene activity across those sets. 

Seehawer and his colleagues did just that in the new study. They began with two collections of mouse breast cancer cells: one in which KMT2C and D were normal, and one in which they were knocked out. Using an array of experimental techniques, they searched the samples for several types of histone markers. 

One difference stood out. Cells with knocked-out KMT2C and D had much more of a protein called KDM6A bound to histones than cells with normal KMT2C and D did. An increase in KDM6A can have a stimulatory effect on certain genes. In the case of cells with knocked-out KMT2C and D, the gene that gets amped up is Mmp3, researchers found. 

There’s good reason for thinking that overactive Mmp3 endows breast cancer cells with the restlessness that sends them to the brain. For one, MMP-3 (the protein made from Mmp3) is a protease, an enzyme that breaks down proteins and can enable cancer cells to barge through surrounding tissue. For another, researchers found that tumor samples from patients with triple-negative breast cancer carrying KMT2C mutations have high levels of MMP-3. 

The case against Mmp3 hyperactivity as a key factor in brain metastasis in triple-negative breast cancer was strengthened when researchers used a drug agent to block KDM6A in animal models of the disease. The effect was to lower the activity of Mmp3 and prevent brain metastasis in the animals. 

“Our results point to KDM6A as a key mediator of brain metastasis in triple-negative breast cancers harboring mutations in KMT2C and D,” Polyak says. Although MMP-3 itself is probably not a good target for therapies to prevent brain metastasis, as MMP-3 inhibitors can be quite toxic, agents that target KDM6A may be more successful. The development of such agents is a first step toward clinical trials in patients. 

About the Medical Reviewer

Kornelia Polyak, MD, PhD, is a Professor of Medicine at Dana-Farber Cancer Institute, Harvard Medical School, and a co-leader of the Dana-Farber Harvard Cancer Center Cancer Cell Biology Program.  Dr. Polyak is an internationally recognized leader of breast cancer research.  Her laboratory is dedicated to improving the clinical management of breast cancer patients by understanding molecular and cellular determinants of breast cancer risk and tumor evolution.  Dr. Polyak has devoted much effort to develop new ways to study tumors and to apply interdisciplinary approaches.  Dr. Polyak has received numerous awards including the Paul Marks Prize for Cancer Research, AACR Outstanding Investigator Award for Breast Cancer Research, and the 14th Rosalind E. Franklin Award for Women in Science.  She is a recipient of the NCI Outstanding Investigator award (2015 and 2022) and received a Distinguished Alumna Award from Weil-Cornell in 2020.  Dr. Polyak was the American Association for the Advancement of Science Fellow in 2019, member of the Fellows of the AACR Academy in 2020, and to the National Academy of Sciences and the National Academy of Medicine in 2022.  She was also a recipient of the American Cancer Society Research Professor Award in 2022 and received the 2023 AAACR Distinguished Lectureship in Breast Cancer Research award.