A groundbreaking study has identified the first inherited genetic marker that predicts resistance to immunotherapy in metastatic melanoma, potentially solving a decade-long mystery of why nearly half of patients with the deadliest form of skin cancer fail to respond to checkpoint inhibitor treatments.
Researchers led by NYU Langone Health and its Perlmutter Cancer Center analyzed genetic material from 1,225 patients with metastatic melanoma participating in the landmark CheckMate-067 phase 3 trial. Their findings, published in Nature Medicine, revealed that patients carrying a specific mitochondrial DNA variant called haplogroup T (HG-T) were 3.46 times less likely to respond to checkpoint immunotherapy compared to patients with other mitochondrial haplogroups.
Mitochondrial Genetics Drive Treatment Resistance
The study focused on mitochondrial DNA, which differs from nuclear DNA by being inherited exclusively from mothers. Mitochondria serve as cellular energy centers and play crucial roles in immune cell development. The HG-T variant was found in approximately 12% of metastatic melanoma patients in the study.
"This research fundamentally changes our understanding of mitochondrial genetics in immune response biology and personalized cancer immunotherapy," said senior study investigator Tomas Kirchhoff, PhD, an associate professor in the Department of Population Health at NYU Grossman School of Medicine. "It also suggests that variations in mitochondrial DNA could have impact beyond melanoma and apply to checkpoint treatments of other cancers."
The CheckMate-067 trial tested frontline use of checkpoint inhibitors nivolumab alone or in combination with ipilimumab. While both regimens proved effective in more than 50% of all treated patients, the response rate plummeted to just 18% in patients carrying the HG-T variant.
Validation Across Multiple Cancer Centers
To confirm their findings, researchers validated results using samples from 675 metastatic melanoma patients treated at 13 cancer centers participating in the International Germline Immuno-Oncology Melanoma Consortium (IO-GEM). This additional analysis confirmed the same association between HG-T and immunotherapy resistance.
"Our study offers the first scientific evidence of an inherited genetic marker, the presence of mitochondrial haplogroup T, as a means of identifying those metastatic melanoma patients who are least likely to respond to immunotherapy treatment," said study co-lead investigator Kelsey Monson, PhD.
Mechanism of Resistance Revealed
The research uncovered biological mechanisms underlying the treatment resistance. Patients with HG-T had more underdeveloped T cells in their blood compared to non-resistant patients. Researchers traced this poor T cell differentiation to increased resilience to reactive oxygen species (ROS), toxic chemicals primarily produced by mitochondria.
The findings suggest that HG-T conferred protection against ROS that stunted T cell attacks against tumors. Checkpoint inhibitors work by blocking interactions between cancer cells and checkpoint proteins on immune T cells, preventing T cells from becoming inactivated and enabling continued cancer cell attack.
Clinical Implications and Future Directions
The discovery opens possibilities for pre-treatment genetic testing to identify patients unlikely to benefit from standard checkpoint therapy.
"Our findings make possible the clinical testing for the presence of mitochondrial haplogroup T to determine nonresponding patients before they start immunotherapy, so other treatment combinations can be considered," said study co-lead investigator Robert Ferguson, PhD. "This in turn could improve patient survival."
The research team plans to conduct prospective clinical trials to assess whether non-HG-T patients demonstrate superior outcomes on immunotherapy compared to HG-T carriers, and whether similar patterns apply to other mitochondrial haplogroups and cancer types.
Metastatic melanoma kills nearly 10,000 Americans annually. The CheckMate trial involved more than 100 medical centers across 19 countries, with both nivolumab and ipilimumab manufactured by Bristol Myers Squibb, which sponsored the trial and provided patient specimens and data for the analysis.
The study received funding from National Institutes of Health grants and additional support from the Melanoma Research Alliance and Italian Ministry of Health grants.
