Mitochondrial RNA May Explain How Tumors Become Resistant to Immunotherapy

By Dr. Chinta SidharthanReviewed by Laura ThomsonSep 22 2026

Interferons are immune signaling cytokines that help destroy malignant cells, and yet these same cytokines sometimes switch sides and help tumors grow by allowing them to dodge the immune system. In a recent study published in Science, a team at the Salk Institute traced this role reversal to the mitochondrial ribonucleic acid (mtRNA) inside cancer cells. The discovery could open new paths for overcoming immunotherapy resistance.

Interferons are versatile immune signaling proteins that mobilize immune cells to seek out and destroy cancer cells.

Oncological research has incorporated interferons since 2011 via immunotherapies, and these treatments have transformed outcomes for many patients. Even so, a substantial share of tumors either fails to respond to these therapies or develop resistance after initial success.

Part of the difficulty stems from interferon signaling's dual nature. Brief exposure to interferons generally supports tumor elimination, but sustained exposure can trigger opposing effects that dampen immune activity within the tumor microenvironment.

Although researchers have described this shift in earlier studies, the specific cellular events that push interferons from an anti-tumor role toward a pro-tumor one remain poorly understood.

About the Study

The team exposed a mouse melanoma cell line to either type I interferon or type II interferon for 24 hours (acute exposure) or 28 days (chronic exposure). They measured cell proliferation under each condition and transferred the treated cells into mouse flanks to track tumor growth over time. In a related experiment, they injected some treated cells into the spleen to assess whether they could spread to the liver. The researchers also profiled immune cell populations within the resulting tumors.

To investigate the molecular basis of these effects, the researchers performed ribonucleic acid (RNA) sequencing and chromatin accessibility mapping on treated cells, and then built a custom analytical approach to identify genes specifically associated with each interferon type. They also conducted protein-deoxyribonucleic acid (DNA) binding assays to examine how transcription factors linked to interferon signaling occupied the genome under each treatment condition.

The team then generated cell lines lacking specific innate immune signaling proteins, including receptors and sensors that detect nucleic acids in the cytoplasm, to determine which components were required for the chronic-exposure response. They used chemical inhibitors to block mitochondrial gene transcription and a channel protein that releases mitochondrial contents into the cytoplasm. They then used confocal microscopy and fluorescent probes to visualize immune signaling protein clustering and detect mitochondrial genetic material outside mitochondria.

The researchers also assessed mitochondrial function and used mass spectrometry to measure the lipid signaling molecules secreted by treated cells. Finally, they generated and tested cells lacking the enzymes involved in producing these lipids in mice, along with an antibody-based immunotherapy, tracking tumor response across multiple rounds of treatment and cell re-implantation.

Key Findings

The study found that prolonged, rather than brief, exposure to type II interferon caused melanoma cells to grow more aggressively once implanted in mice, despite interferons being known primarily for their anti-tumor effects. This chronic exposure also led to the tumor spreading to the liver and altered the immune cell composition of the tumor environment in ways consistent with suppressed immune activity, including fewer monocytes, more neutrophils, and reduced immune cell function.

Further investigation revealed that chronically treated melanoma cells released genetic material from their mitochondria into the surrounding cell fluid. Internal sensors that normally guard against viral infection picked up this material, prompting the cell to produce type I interferon even though no virus was present. The two interferon signals then worked together to increase cyclooxygenase 2 activity, an enzyme that produces prostaglandin E2, a lipid molecule known to suppress immune activity.

However, blocking either the sensing pathway or the release of mitochondrial material prevented this secondary interferon response. Furthermore, eliminating the cell's capacity to produce prostaglandin E2, either through a common anti-inflammatory drug or by removing the relevant enzymes, reversed the enhanced tumor growth caused by chronic interferon exposure and restored a more active immune profile within the tumor.

The effect also extended to therapy resistance. Melanoma cells that had stopped responding to antibody-based immunotherapy showed elevated cyclooxygenase 2 activity, and removing it restored sensitivity to treatment in nine of 10 mice, with tumors regressing completely. Moreover, the pattern held across several mouse melanoma cell lines and in human melanoma cells, suggesting the mechanism is not confined to a single model system.

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Conclusion

The study uncovered a previously unrecognized route involving mtRNA by which prolonged interferon II exposure shifts anti-cancer immune activity to a pro-cancer profile. These findings are significant, given the substantial portion of tumors that stop responding to immunotherapy.

The findings showed that interrupting this mtRNA-based pathway can restore sensitivity to immunotherapy in resistant tumors. The study points toward a potential strategy for improving outcomes in patients whose cancers no longer respond to existing checkpoint-based treatments.