A Single tRNA Molecule Controls Whether Prostate Cancer Stays Vulnerable to Therapy

Transfer RNAs have long been viewed as the humble workhorses of the cell, ferrying amino acids to the ribosome without any say in a cell’s identity or fate. A new study published in Nature upends that assumption. Researchers led by Yeon Soo Kim and Andrew C. Hsieh at the Fred Hutchinson Cancer Center, together with Tao Pan at the University of Chicago and collaborators across multiple institutions, report that the dosage of a single transfer RNA species, tRNA1Arg(UCU), acts as a molecular switch governing whether prostate cancer cells remain dependent on androgen receptor signaling or escape into a drug-resistant, lineage-plastic state. The finding reveals an unexpected layer of gene regulation in which codon biology directly shapes cancer cell identity and treatment response.

Prostate cancer is the archetypal lineage-dependent malignancy. Its growth hinges on the androgen receptor (AR), which is why androgen deprivation therapy and second-generation AR pathway inhibitors such as enzalutamide, apalutamide and darolutamide form the backbone of advanced disease treatment. Yet resistance is nearly universal. Tumors frequently shed their AR dependence through a process called lineage plasticity, transdifferentiating into neuroendocrine-like states that no longer respond to AR-targeted drugs. Genetic loss of TP53, PTEN or RB1 can drive this transition, but the translational mechanisms, the events at the level of protein synthesis, that permit such phenotypic flexibility have remained largely unknown.

To find them, the team performed unbiased small RNA sequencing using a multiplex platform capable of quantifying full-length tRNAs, their fragments and selected chemical modifications. They applied this technique to an engineered model in which LNCaP prostate adenocarcinoma cells were pushed into a lineage-plastic state through RB1 knockdown and overexpression of mutant TP53, MYCN, ASCL1, SRRM4, NR0B2, BCL2 and mutant KRAS. Among 49 tRNA isoacceptor families surveyed, only tRNAArg(UCU) was significantly downregulated during the transition, with a log2 fold change of roughly minus 0.34 and a false discovery rate of 2.42 x 10-25 in one analysis. Within the five tRNAArg(UCU) isodecoders, molecules sharing the same anticodon but differing in body sequence, tRNA1Arg(UCU) was the most abundant and the only one substantially decreased. Northern blotting and quantitative PCR confirmed the reduction in both LNCaP and C4-2B cells, and the decline was not accompanied by changes in tRNA fragmentation or chemical modification, indicating a specific loss of the mature molecule.

The correlation with lineage identity was striking. Across nine prostate cancer cell lines, tRNA1Arg(UCU) abundance showed a strong positive correlation with AR activity (Pearson’s r = 0.85, P = 0.0034) and a negative correlation with the neuroendocrine markers ENO2 and SCN3A. In the LTL331 patient-derived xenograft model, which transdifferentiates from adenocarcinoma to neuroendocrine prostate cancer after castration, tRNA1Arg(UCU) levels fell in a stepwise fashion from pre-castration through castration to relapse. The researchers then developed an in situ hybridization assay to visualize the tRNA directly in patient tissue. In specimens from 56 patients in the University of Washington rapid autopsy cohort, AR-positive tumors expressed significantly higher levels of tRNA1Arg(UCU) than neuroendocrine-positive tumors, and tRNA abundance correlated positively with AR activity and negatively with the neuroendocrine marker ELAVL4.

Crucially, the tRNA was not merely a passive marker. Using inducible short hairpin RNAs, the team reduced tRNA1Arg(UCU) levels by 25 to 50 percent in LNCaP and C4-2B cells. The knockdown was specific, leaving other tRNAArg(UCU) isodecoders untouched. The consequence was a coordinated shift in cell identity: AR pathway genes declined at both RNA and protein levels, while neuron-related gene programs rose. Cells depleted of the tRNA became significantly more resistant to enzalutamide, apalutamide and darolutamide, yet more sensitive to alisertib, an Aurora kinase A inhibitor with activity in neuroendocrine prostate cancer. In mice, the team generated animals haploinsufficient for n-Trtct2, the gene encoding tRNA1Arg(UCU), crossed onto the MYC-driven Hi-Myc prostate cancer model. Organoids derived from these mice showed a threefold increase in resistance to AR inhibition, and after surgical castration, haploinsufficient mice developed significantly enlarged prostates, with 25 percent exhibiting high-grade prostatic intraepithelial neoplasia compared with none of the controls.

Most remarkably, the process proved reversible. Re-expressing tRNA1Arg(UCU) in lineage-plastic cells restored AR pathway gene expression, suppressed neuroendocrine markers and resensitized the cells to AR-targeted therapies. Overexpression of other arginine tRNA isodecoders or isoacceptors had no such effect, underscoring the exquisite specificity of this single molecule. In LNCaP-abl cells, a subline that spontaneously evolved androgen insensitivity after prolonged culture in androgen-depleted medium, restoring tRNA1Arg(UCU) enhanced AR signaling and improved enzalutamide sensitivity. In the TRAMP transgenic mouse model, which normally progresses toward neuroendocrine tumors, crossing in a tRNA1Arg(UCU) overexpression allele reduced the incidence of premalignant glands after castration. Together, these experiments demonstrate that lineage dependency in prostate cancer can be toggled by modulating one tRNA species.

The team then asked how tRNA1Arg(UCU) is regulated. Mining the ENCODE database of transcription factor binding, they identified 11 DNA-binding proteins that occupy the TRR-TCT1-1 genomic locus encoding the tRNA. Four of these were downregulated during lineage transition, and functional screening pinpointed two: TARDBP, a DNA- and RNA-binding protein best known for its role in amyotrophic lateral sclerosis, and ZSCAN29, a zinc-finger protein. Silencing either factor reduced tRNA1Arg(UCU) expression, and their occupancy, measured by CUT&RUN profiling, declined selectively at the TRR-TCT1-1 locus during lineage plasticity. The locus carried the highest enrichment of the H3K4me3 histone mark among all six TRR-TCT isodecoder genes, and this mark, along with RNA polymerase III occupancy, was lost specifically at TRR-TCT1-1 during the lineage switch. TARDBP and ZSCAN29 appear to maintain RNA polymerase III recruitment at this chromatin-primed locus, and their expression correlated with tRNA1Arg(UCU) levels in patient specimens. This work provides one of the first demonstrations of isodecoder-specific transcriptional control of tRNA genes in cancer, extending tRNA regulation beyond canonical RNA polymerase III mechanics.

How does a single tRNA change cell fate? The answer lies in codon optimality. tRNA1Arg(UCU) decodes the AGA arginine codon, and the researchers built fluorescent reporters to show that translational capacity at AGA codons dropped roughly fourfold in lineage-plastic cells and was restored by tRNA addback. Polysome RNA sequencing, which separates ribosome-bound messenger RNAs by density to measure translation efficiency genome-wide, revealed that AGA codons were enriched among efficiently translated transcripts in adenocarcinoma cells, lost that enrichment in lineage-plastic cells, and regained it upon tRNA restoration. Among the translationally upregulated targets were five components of the SWI/SNF chromatin remodeling complex, and the team focused on SMARCC2, whose protein levels fell during lineage transition despite unchanged mRNA. A codon-switching experiment confirmed the mechanism: replacing SMARCC2’s AGA codons with synonymous CGC codons rendered the protein insensitive to lineage state. Silencing SMARCC2 in tRNA-restored cells reversed the AR pathway reactivation and restored enzalutamide resistance, establishing SMARCC2 as a key translational mediator through which tRNA1Arg(UCU) sustains lineage fidelity.

The clinical implications are substantial. In the rapid autopsy cohort, patients with the lowest tRNA1Arg(UCU) abundance had significantly shorter time to first bone metastasis, shorter survival after starting androgen deprivation therapy, shorter survival after developing androgen independence, and shorter overall survival overall. In mouse models, tRNA depletion led to a fourfold increase in metastatic burden following intracardiac injection of luciferase-labeled cells. The authors caution that the clinical associations are retrospective and that prospective studies will be needed to validate tRNA isodecoders as biomarkers of AR-targeted therapy resistance. But the therapeutic horizon is already visible: adeno-associated virus delivery of suppressor tRNAs has restored protein function in models of mucopolysaccharidosis type I, and lipid nanoparticle-based tRNA delivery has re-expressed CFTR in cystic fibrosis epithelia. Such platforms could, in principle, be adapted to restore tumor-suppressive tRNAs like tRNA1Arg(UCU), reprogramming lineage dependency and resensitizing tumors to existing therapies. For a disease in which treatment resistance remains the central clinical challenge, the idea that a single RNA adaptor molecule holds a master key to cellular identity is a genuinely paradigm-shifting proposition.

Subject of Research: Regulation of prostate cancer lineage plasticity and therapy resistance by tRNA dosage

Article Title: tRNA dosage regulates lineage dependency and resistance in prostate cancer

Article References: Kim, Y. S., Arora, S., Young, D., Tsou, A., Shiuan, A., Wladyka, C. L., Rudoy, D., Kim, J. Y., Waters, J. A., Schuster, S. L., Coleman, I. M., Kapur, M., Sobczyk, M., Katanski, C. D., Bayat Tork, A. M., Zhang, W., Nelson, P. S., Ha, G., Haffner, M. C., … Hsieh, A. C. (2026). tRNA dosage regulates lineage dependency and resistance in prostate cancer. Nature. https://doi.org/10.1038/s41586-026-11153-8

Image Credits: AI Generated

DOI: 10.1038/s41586-026-11153-8

Keywords: prostate cancer, transfer RNA, lineage plasticity, androgen receptor, therapy resistance, neuroendocrine prostate cancer, translation, SMARCC2, TARDBP, ZSCAN29, RNA polymerase III, codon optimality