Getting around cancer work-arounds in immunotherapy

In a study published Sept. 24 in Nature Communications, the Fred Hutch scientists used a new method for measuring molecules in single cells—single-cell RNA sequencing, to be exact—to deeply analyze the response to a combination immunotherapy for patients with Merkel cell carcinoma, a rare skin cancer caused by a common virus.

“Twenty percent of Merkel cell patients have an initial response to immunotherapy, but then relapse—it’s been unclear why,” said first author Dr. Kelly Paulson, a senior fellow at Fred Hutch. “Understanding the cause of relapse allows us to design immunotherapies that can get toward long-term tumor control to make cancer a more chronic disease.”

And so it happened that Paulson and senior author Dr. Aude Chapuis, an assistant member of Fred Hutch, looked at cancer cells from two patients who initially responded to a combination therapy that combined a checkpoint inhibitor and a T cell therapeutic.

Initially, and not surprisingly, the tumors shrank in response to the therapy.

“We saw in both patients that the cancers went almost completely away,” said Paulson, who cares for patients at Fred Hutch’s clinical care partner, Seattle Cancer Care Alliance. “The cancers were shrinking, and when we took biopsies we saw that the T cells actually got into the cancers and helped mediate this regression. That was exciting, and the patients were doing great.”

One patient was nearly ready to go into hospice care but ended up healthy enough to return to work instead; however, about two years later, things changed.

“It turned out to be metastatic Merkel cell cancer,” Paulson said. “It grew quickly, it was biopsied and shortly after it showed up in multiple places.”

In the second patient, the cancer returned as well, but in an isolated spot—that cancer is still being controlled and hasn’t spread any farther.

In neither patient was there a clearly discernible reason as to why the cancer came back.

So Paulson and Chapuis, in collaboration with coauthors Dr. Paul Nghiem of the University of Washington and Fred Hutch’s Dr. Jason Bielas and Dr. Raphael Gottardo, put single-cell RNA sequencing to work to take a close look at molecular changes in T cells, tumor cells and all other cells in the tumor microenvironment to see what had changed.

“By doing this, we were able to see that the tumor was hiding specifically from the T cells,” Paulson explained.

It did this by hiding a biomarker, doing so by removing one piece of a trio of genes—human leukocyte antigens (HLAs)—that allow the T cells in the combo immunotherapy to find the cancer cells.

The HLAs usually all turn off or on at the same time, the researchers note, and traditional methods measure HLA as a group. As a result, that caused the act of a single gene being turned off to be undetectable. The single-cell RNA sequencing technology, however, revealed that that missing piece that made the cancer cells invisible to the T cells and able to grow and spread anew.

Of course, identifying the problem is only half of the challenge, and so Paulson says that she cultured cells from one of the patients and applied drugs already used clinically for other cancers that turned the cancer marker back on. The researchers are currently testing various combinations of therapies that could be used for patients who relapse in this particular manner.

“It’s absolutely revelatory,” Chapuis said of the findings. “We didn’t know what was going on with these patients and how their cancer was able to come back. Now we are able to understand what’s going wrong, and that gives us a way to fix it. It’s very obvious we need a multi-pronged approach, rather than just one dagger that the cancer can escape.”

An important caveat to this potential new therapeutic approach and the specific nature of its application is noted in the discussion portion of the team’s published research, when they note: “Immunotherapy escape by genetic HLA loss is important to distinguish from immunotherapy escape by transcriptional HLA loss as we observed here. In the former, the HLA alleles are deleted and new T cell responses must necessarily be targeted to alternate HLAs to overcome immunotherapy resistance. In the latter, tumor-specific HLA suppression is potentially reversible with drug therapy.”

The team also acknowledged limitations to their research aside from simply the small sample size, noting that “Attempts to generate tumor-derived cell lines for additional functional studies were unsuccessful on both patients. We could not differentiate if acquired resistance represented immunoediting, i.e., outgrowth of a pre-existing previously rare or quiescent clone, or was new transcriptional suppression that developed after immunotherapy. In either scenario, immune pressure from the transferred CD8+ T cells revealed selective HLA downregulation that was transcriptional, and in at least one patient, reversible.”

But limitations aside—and the need for further and broader research being obvious—the Fred Hutch findings could go a long way toward pushing immuno-oncology treatments out ahead of cancers' adaptive abilities to evade them.