NEW YORK (GenomeWeb) – Researchers from the US and the Netherlands reported in the New England Journal of Medicine that they have identified mutations in immune system-related genes in individuals who initially responded to anti-PD-1 treatment for metastatic melanoma treatment, but relapsed after six months or more.
A team led by investigators at the University of California at Los Angeles, the Jonsson Comprehensive Cancer Center, and the Netherlands Cancer Institute did exome sequencing on tumor samples from four individuals with metastatic melanoma prior to treatment with pembrolizumab (marketed as Keytruda by Merck). The researchers also assessed protein-coding sequences in tumor samples taken after late relapse, comparing the baseline and relapse tumors to search for mutations related to checkpoint blockade therapy resistance.
They uncovered suspicious mutations in three of the four individuals. In one individual, for example, they saw a truncating mutation affecting the beta-2-microglobulin (B2M) gene, which contributes to expression of class I major histocompatibility complex molecules recognized by the immune system's CD8 T cells. Two more relapse tumors contained loss-of-function mutations to JAK1 or JAK2 — genes coding for interferon-related kinase enzymes.
"The mutations make the tumor resistant to the way the immune system tries to kill it," first author Jesse Zaretsky, an MD/PhD student in senior author Antoni Ribas' University of California at Los Angeles lab, told GenomeWeb. For example, he explained, the JAK mutations "are associated with the interferon receptor and make the tumors insensitive to the signals the immune system sends to slow [tumor] growth and kill the cancer."
While roughly three-quarters of individuals treated with anti-PD-1 therapies show durable treatment responses, acquired resistance can occur, even long after immunotherapy-mediated tumor regression.
"With the approval of PD-1 checkpoint blockade agents for the treatment of patients with melanoma, lung cancer, and other cancers, it is anticipated that cases of late relapse after initial response will increase," the study's authors wrote. "Understanding the molecular mechanisms of acquired resistance … may open options for the rational design of salvage combination therapies or preventative interventions and may guide mechanistic biomarker studies for the selection of patients, before the initiation of treatment, who are unlikely to have a response."
The team started with 78 metastatic melanoma patients who were treated with pembrolizumab at UCLA. Of the 42 individuals who showed an objective response to the checkpoint blockade therapy, 15 eventually experienced disease progression.
From that group of 15 patients, the researchers focused on four patients with late-acquired resistance — six months or more after response to pembrolizumab as a single agent — for whom there was sufficient biopsy material and clinical information available. Each of the patients had been receiving continuous doses of the drug until relapse, which occurred after a mean of nearly 21 months.
When the investigators scrutinized biopsies from the relapse tumors, they saw enhanced PD-L1 expression at the edges of tumors, along with CD8 T cells attempting to infiltrate the tumors. After capturing protein-coding portions of the genome in baseline and relapse tumor samples with Nimblegen exome kits, the team sequenced the exomes to nearly 150-fold average coverage using the Illumina HiSeq 2000.
"We wanted to capture all of the mutations down to low allele frequencies to get a picture of everything that was going on in the tumors, both before they went on the treatment and after [the tumors] came back," Zaretsky said.
In the two cases marked by new JAK1 or JAK2 mutations at relapse, the team found that 93 percent to nearly 96 percent of baseline tumor mutations persisted in the relapse tumors.
The researchers suspect resistance mutations arose from clonal populations in the metastatic tumors that expanded after anti-PD-1 treatment. From allele frequency patterns in the relapsed tumors with JAK1/2 mutations, for example, they concluded that "tumors resistant to anti-PD-1 are a relatively homogeneous population derived directly from the baseline tumor and that acquisition of the JAK mutations was an early founder event."
Even so, they didn't detect burgeoning resistance mutations in the pre-pembrolizumab-treatment tumors, Zaretsky said, perhaps because such alterations were present in very few cells in the baseline tumors.
In cell lines established from the individual with JAK2 loss-of-function mutations at relapse, the team's NanoString Technologies' nCounter expression experiments pointed to loss of JAK2 protein expression after treatment progression, along with a dip in interferon gamma activity and diminished production of proteins involved in antigen presentation and T cell activity.
Zaretsky noted that larger studies are needed to see if the same sorts of mutations identified in the initial study of relapsed metastatic melanoma patients are common in other patients who eventually progress after checkpoint blockade therapy — and to find other potential resistance-related mutations.
For their part, the researchers are currently generating cell line models to study mechanisms for the resistance mutations found so far, in the hopes of finding ways to prevent relapse.