Anticancer drugs called checkpoint blockade inhibitors have proven effective in some cancer patients. These drugs suppress the body's T cell response and stimulate these immune cells to destroy tumors. Some studies have shown that these drugs work better in patients whose tumors have large amounts of mutated proteins, which scientists believe is because these proteins provide T cells with a large number of targets to attack. However, for at least 50% of patients whose tumors have a high mutational burden, checkpoint blockade inhibitors do not work at all.
In this colon tumor, which is highly deficient in DNA mismatch repair due to mutations, T cells (labeled black, green, and red) mainly accumulate in supporting tissue (pink area), and only a few infiltrate into the tumor cells (islands surrounded by supporting tissue). Image source: Provided by researchers
A new study from MIT reveals a possible explanation. In a study of mice, researchers found that measuring the diversity of mutations within a tumor was a more accurate predictor of whether a treatment would be successful than measuring the overall number of mutations.
If validated in clinical trials, this information could help doctors better determine which patients would benefit from checkpoint blockade inhibitors.
"Immune checkpoint therapies, while very effective under the right circumstances, are not effective in all cancer patients. This study clearly demonstrates the role of cancer genetic heterogeneity in determining the effectiveness of these therapies," said Tyler Jacks, the David Koch Professor of Biology and a member of MIT's Koch Institute for Cancer Research.
Jacks, Peter Westcott, a former MIT postdoc in Jacks' lab and now an assistant professor at Cold Spring Harbor Laboratory, and Isidro Cortes-Ciriano, research group leader at EMBL European Bioinformatics Institute (EMBL-EBI), are the senior authors of the paper, which was published in the journal Nature Genetics on September 14.
mutational diversity
Across all types of cancer, a small subset of tumors have what's called a high tumor mutational burden (TMB), meaning they have a very high number of mutations in each cell. A subset of these tumors have DNA repair defects, most commonly DNA mismatch repair.
Because these tumors have so many mutated proteins, they are considered ideal candidates for immunotherapy treatment because they provide T cells with a large number of potential targets to attack. In the past few years, the FDA approved a checkpoint blockade inhibitor called pembrolizumab, which activates T cells by blocking a protein called PD-1, to treat several tumors with high TMB.
However, subsequent studies of patients treated with this drug found that more than half of them responded poorly or showed only transient responses, despite their tumors having a high mutational load. The MIT team designed mouse models that closely mimic the development of tumors with high mutation loads to begin exploring why some patients respond better than others.
These mouse models carry genetic mutations that drive the development of colon and lung cancer, as well as a mutation that shuts down the DNA mismatch repair system when these tumors begin to develop. This causes the tumor to develop many additional mutations. When the researchers treated these mice with checkpoint blockade inhibitors, they were surprised to find that none of the mice responded well to the treatment.
"We verified that we were inactivating DNA repair pathways very effectively, resulting in a large number of mutations," Westcott said. "These tumors looked just like human cancers, but they were not more infiltrated by T cells and did not respond to immunotherapy."
intratumoral heterogeneity
The researchers found that the lack of response appeared to be due to a phenomenon called intratumoral heterogeneity. This means that while tumors have many mutations, each cell in the tumor tends to have mutations that are different from those of most other cells. Therefore, each cancer mutation is "subclonal," that is, expressed in a small number of cells. (Clonal "mutation" means expressed in all cells).
In further experiments, the researchers explored conditions that altered lung tumor heterogeneity in mice. They found that checkpoint blockade inhibitors were highly effective in tumors with clonal mutations. However, when they increased heterogeneity by mixing tumor cells with different mutations, they found that the treatment became less effective.
"This shows us that intratumoral heterogeneity actually interferes with the immune response, and it's only in clonal tumors that you really get a robust immune checkpoint blockade response," Westcott said.
Failed to activate
The weak T-cell response appears to occur because the T cells simply do not see enough of the specific cancer protein or antigen to become activated, the researchers said. When researchers implanted mice with tumors containing subclonal-level proteins, the proteins often elicited strong immune responses, but the T cells failed to become strong enough to attack the tumors.
"You can have these highly immunogenic tumor cells that are supposed to result in a profound T cell response, but at this low clonal level they become completely invisible and the immune system cannot recognize them," Westcott said. "The T cells don't recognize enough of the antigen, so they're not primed enough to acquire the ability to kill the tumor cells."
To see whether these findings could be generalized to human patients, the researchers analyzed data from two small clinical trials in patients with colorectal or gastric cancer who were treated with checkpoint blockade inhibitors. After analyzing the sequences of patients' tumors, they found that patients whose tumors were more uniform responded better to treatment.
Conclusion and Enlightenment
"Our understanding of cancer continues to improve, which is leading to better outcomes for patients," said Cortes-Ciriano. "Thanks to advanced research and clinical studies, survival rates after a cancer diagnosis have improved significantly over the past 20 years. We know that every patient's cancer is different and requires a tailored approach. Personalized medicine must take into account new research that is helping us understand why cancer treatments work for some patients but not all."
The researchers say the findings also suggest that treating patients with drugs that block DNA mismatch repair pathways in the hope of creating more mutations that T cells can target may not help, and may instead be harmful. One of the drugs is currently in clinical trials.
"If you try to mutate an existing cancer that already has many cancer cells at the primary site and others that may have spread throughout the body, then you create a super heterogeneous collection of cancer genomes. Our results show that because of high intratumoral heterogeneity, T cell responses are disorganized and completely unresponsive to immune checkpoint therapy."