Cancer cells recruit RNA editors and tRNA modifiers to survive immune attack

When the immune system closes in on a tumour, it does more than send killer cells to the front line. Activated T cells flood the tumour microenvironment with interferon-gamma, a signalling molecule that forces cancer cells to activate an enzyme called IDO1, which destroys their supply of the essential amino acid tryptophan. Starved of a fundamental building block, many tumour cells would be expected to grind to a halt. Instead, a new study published in Nature Cell Biology reveals that cancer cells respond with a remarkable act of molecular improvisation: they deliberately corrupt their own protein-making machinery, swapping tryptophan for the chemically similar phenylalanine and producing a wave of aberrant proteins from perfectly intact genes. The research, led by Demi Wernaart and Amos Fumagalli in the laboratory of Reuven Agami at the Netherlands Cancer Institute, identifies two RNA-modifying enzymes, ADAR1 and FTSJ1, as the genetic puppeteers behind this process, and shows that tumours elevate both to survive the metabolic siege imposed by anti-tumour immunity.

The phenomenon at the heart of the study is called mistranslation. Ribosomes, the molecular machines that read messenger RNA and assemble proteins, normally interpret each three-letter codon with high fidelity. But when tryptophan runs short, two distinct errors emerge. In one, ribosomes stall at tryptophan codons and slip out of their reading frame, generating entirely different protein sequences from unaltered mRNA, a behaviour the field has dubbed translational sloppiness. In the other, a subtler and arguably stranger process, the tryptophan-transfer RNA is misloaded with phenylalanine, so the ribosome inserts the wrong amino acid while continuing to read the message in frame. The resulting proteins, termed W>F substitutants, carry phenylalanine wherever tryptophan should have been. Previous work had shown that these substitutants accumulate in tumours and correlate with T cell activity, but whether they were merely inevitable accidents of a stressed translation apparatus or actively regulated by the cancer cell’s genome remained an open question.

To answer it, the team built an elegant genetic tool. Their dual-reporter vector places a single tryptophan codon inside the sequence of SIINFEKL, a well-studied peptide that is displayed on the cell surface by the mouse H-2Kb major histocompatibility complex when correctly produced. Downstream, in a different reading frame, sits a turbo-green fluorescent protein that can only be expressed if the ribosome frameshifts at that same tryptophan codon. The system therefore reports both mistranslation modes simultaneously: surface presentation of SIINFEKL signals tryptophan-to-phenylalanine substitution, while green fluorescence signals frameshifting. When the researchers introduced this construct into A549 lung cancer cells and treated them with interferon-gamma, tryptophan-free medium, or both, they observed strong SIINFEKL induction under conditions that depleted tryptophan, and mass spectrometry confirmed that endogenous cellular proteins carried the same W>F substitutions. By comparing peptide intensities, they estimated the median extent of mistranslation at roughly one percent of the relevant proteome, a strikingly high error rate for a process once assumed to be vanishingly rare.

With the reporter validated, the team launched a genome-wide CRISPR-Cas9 knockout screen using the Brunello library, treating the cells with interferon-gamma plus tryptophan depletion and then sorting, by fluorescence-activated cell sorting, the rare cells that retained frameshifting but had lost SIINFEKL presentation. This strategy filtered out genes affecting tryptophan levels or reporter expression and homed in on factors specific to codon reassignment. Alongside expected hits such as WARS1, the tryptophanyl-tRNA synthetase, and antigen-presentation genes including B2M and TAP1, the screen surfaced two unexpected candidates: ADAR1, an adenosine-to-inosine RNA-editing deaminase, and FTSJ1, a 2′-O-methyltransferase that decorates the anticodon loops of several transfer RNAs. Neither had previously been implicated in mistranslation, and their emergence suggested that cancer cells actively invest in the machinery of translational error.

The two enzymes turned out to operate through fundamentally different mechanisms. ADAR1, the team found, is a global enabler of mistranslation. This enzyme resolves double-stranded RNA structures by converting adenosine to inosine, thereby preventing the activation of antiviral sensors such as protein kinase R that would otherwise shut down protein synthesis. When the researchers knocked out ADAR1, global translation dropped, and W>F substitutant production collapsed even though tryptophan remained depleted and IDO1 remained induced. Crucially, re-expressing a wild-type ADAR1 restored substitutant production, whereas a catalytically dead mutant did not, proving that the editing activity itself is required. Proteomics revealed that ADAR1 loss also suppressed histidine-to-glutamine substitutions under histidine starvation, indicating that its influence extends across multiple mistranslation programmes rather than being confined to tryptophan.

Digging deeper, the researchers connected ADAR1 to the ribosome-associated quality control pathway, or RQC, a conserved system that detects stalled and collided ribosomes and resolves them. Knocking out factors acting at or upstream of ribosome splitting, including ZNF598, RACK1 and ABCE1, suppressed W>F substitutants, while disruption of more downstream effectors had little effect. ADAR1-deficient cells showed reduced protein levels of ZNF598, RACK1 and ABCE1, and the authors propose that ADAR1 sustains the expression of this quality-control machinery, which in turn is essential for the aberrant translation events that flourish under nutrient deprivation. Intriguingly, the interferon-inducible p150 isoform of ADAR1, long known to respond to type I interferons, was also induced by interferon-gamma, a type II interferon central to anti-tumour immunity, hinting at a previously underappreciated role for the enzyme in the tumour-immune battleground.

FTSJ1, by contrast, proved to be a specialist. Loss of the enzyme reduced W>F substitutants without touching global translation, frameshifting, or other known mistranslation events such as histidine-to-glutamine and phenylalanine-to-tyrosine substitutions. Transfer RNA sequencing showed that FTSJ1 loss specifically erased methylation marks at positions 32 and 34 of the tryptophan tRNA anticodon loop, modifications that depend on the cofactors THADA and WDR6 respectively. Catalytically inactive FTSJ1 mutants failed to rescue substitutant production, and the effect was reproduced across lung, glioblastoma, breast, melanoma and prostate cancer cell lines, underscoring the generality of the mechanism. The specificity is remarkable: even though FTSJ1 also methylates the phenylalanine tRNA, phenylalanine-to-tyrosine mistranslation was unaffected, pointing to a uniquely tailored role for the tryptophan tRNA modification.

The biochemical explanation emerged from in vitro experiments with recombinant human WARS1, the synthetase that normally charges tryptophan tRNAs with tryptophan. Under tryptophan scarcity, WARS1 can be tricked into loading phenylalanine instead, but this mischarging is inefficient. Using microscale thermophoresis and aminoacylation assays, the team showed that methylated tryptophan tRNA binds far more readily to phenylalanine-bound WARS1 than does unmethylated tRNA, while binding to tryptophan-bound WARS1 is unaffected by the methylation state. In other words, FTSJ1’s chemical marks act as a molecular handshake that only matters when the enzyme is carrying the wrong amino acid. Normal translation proceeds untouched when tryptophan is abundant, but when the immune system strips tryptophan away, the methylated tRNA is perfectly positioned to accept phenylalanine and keep the protein assembly line running.

The consequences ripple outward to cancer immunology. W>F substitutants generate novel peptides, or neoepitopes, presented on HLA molecules, and some of these, such as the broadly shared TMBIM6 W>F neoepitope, can be recognised by T cells and targeted by adoptive cell therapies. The new study shows that FTSJ1 knockout reduces the presentation of W>F neoepitopes in vitro and in xenograft tumours infiltrated by T cells, and correspondingly dampens T cell activation in co-culture assays. This cuts both ways: on one hand, tumours with high FTSJ1 may diversify their immunopeptidome in ways that could invite immune recognition; on the other, the adaptive benefit of sustaining protein synthesis during tryptophan starvation may outweigh that risk, which may explain why both ADAR1 activity and FTSJ1 expression are elevated in tumour tissues compared with adjacent healthy tissue in clinical proteomics datasets. The authors suggest that phenylalanine’s close resemblance to tryptophan makes these substitutions relatively harmless to the cancer cell, allowing translation to continue while limiting the ribotoxic stress that uncharged tRNAs would otherwise provoke.

The study reframes mistranslation not as noise but as a regulated, multi-layered survival programme that tumours deploy under immune pressure. ADAR1 provides the global permissive environment by maintaining ribosome quality control and suppressing antiviral translational shutdown, while FTSJ1 fine-tunes the tryptophan tRNA to exploit phenylalanine as a surrogate substrate. That two RNA-modifying enzymes converge on the same error pathway suggests the process is controlled at multiple stages, and the authors suspect further regulators remain to be found. Given that substitutant-derived neoepitopes are already being explored as immunotherapy targets, understanding the genetics of their production opens a potential new lever: manipulating ADAR1, FTSJ1 or their cofactors could either amplify the neoepitope supply to energise anti-tumour T cells or throttle the translational escape hatch that tumours rely on when the immune system tightens the metabolic screws.

Subject of Research: Genetic regulation of tryptophan-to-phenylalanine mistranslation in cancer cells under immune-mediated tryptophan depletion

Article Title: Global and specific mechanisms stimulate mistranslation in cancer

Article References: Global and specific mechanisms stimulate mistranslation in cancer. (n.d.). https://doi.org/10.1038/s41556-026-02088-3

Image Credits: AI Generated

DOI: 10.1038/s41556-026-02088-3

Keywords: mistranslation, cancer, ADAR1, FTSJ1, tryptophan depletion, W>F substitutants, ribosome quality control, tRNA methylation, WARS1, interferon-gamma, neoepitopes, translational sloppiness