Cancer cells are voracious builders of ribosomes, the molecular machines that churn out proteins, and to keep pace with their own runaway growth they must synthesize ribosomal RNA at extraordinary rates. That dependence has long made RNA polymerase I (Pol I), the enzyme dedicated to transcribing ribosomal DNA, an attractive drug target. Now a team at Karolinska Institutet reports that JP-1302, an experimental compound originally designed as a brain-penetrating adrenergic receptor antagonist, is a surprisingly potent suppressor of Pol I transcription that dismantles the nucleolus and stalls cancer cell lines at submicromolar to low micromolar concentrations. The study, published in Cell Death Discovery, reveals a compound with a distinctive, dose-dependent dual personality: at low doses it triggers a clean nucleolar stress response without DNA damage, while at higher doses it traps topoisomerases on chromatin and pushes cells into irreversible death.
JP-1302 is a 9-anilinoacridine, a planar tricyclic scaffold shared by classic DNA intercalators such as quinacrine, aminacrine and ethacridine, all of which are known to inhibit Pol I. Its asymmetric anilino tail group, however, places it structurally closer to amsacrine, a clinically used topoisomerase II poison developed for acute leukaemias. The compound was originally engineered as a highly selective alpha-2C-adrenergic receptor antagonist with a favourable lipophilicity profile (logP 4.88 and topological polar surface area of 31.4 square angstroms) that underlies its documented blood-brain barrier penetrance and in vivo activity at tolerated milligram-per-kilogram doses in rodents. A previous proteome-wide screen had flagged JP-1302 as a broad transcriptional perturbagen that suppresses RNA polymerase II phosphorylation at micromolar concentrations, but its effects on Pol I and nucleolar biology had never been examined.
The Karolinska team, led by Mikael Lindström together with Jiri Bartek and colleagues, first mined the DeepCover MOA proteomic dataset and noticed that JP-1302 markedly downregulates POLR1A, the catalytic subunit of Pol I, relative to most other profiled compounds. Resazurin-based profiling across a panel of cancer cell lines of varied origin and p53 status, including osteosarcoma, glioblastoma, colorectal carcinoma, breast cancer and lung adenocarcinoma, plus two non-cancerous lines, revealed growth-inhibitory IC50 values ranging from 0.75 to 4.28 micromolar at 24 hours and 0.13 to 1.63 micromolar at 48 hours. Strikingly, p53-wildtype and p53-knockout HCT116 cells converged to nearly identical IC50 values by 48 hours, suggesting that the growth-inhibitory effect operates largely independently of the tumour suppressor p53.
Immunoblotting then showed that JP-1302 triggers a concentration-dependent depletion of POLR1A protein, evident from around 500 nanomolar and most pronounced at 1 to 5 micromolar after 24 hours. The degradation proved selective: other Pol I subunits and pre-initiation complex components were largely spared, with only POLR1E showing a marginal reduction. Quantitative PCR confirmed that POLR1A messenger RNA was unaltered, pointing to post-transcriptional destruction, and co-treatment with the proteasome inhibitor MG-132 rescued POLR1A levels, confirming proteasome-mediated degradation. Crucially, knocking down the alpha-2C-adrenergic receptor did not affect POLR1A depletion, demonstrating that the compound’s anticancer activity here is entirely independent of the receptor it was designed to block. Notably, POLR2A, the catalytic subunit of Pol II, required higher concentrations of 5 micromolar before its levels declined, underscoring Pol I as the more sensitive target.
With the catalytic subunit under attack, the team measured the primary Pol I transcript, the 47S pre-ribosomal RNA. Quantitative PCR in U2OS osteosarcoma cells showed significant 47S downregulation starting from just 100 nanomolar after 3 hours. To confirm this reflected genuine transcriptional inhibition rather than altered RNA turnover, the researchers used a nascent RNA capture assay based on ethynyl uridine labelling. Nascent 47S rRNA was significantly reduced, while nascent Pol II transcripts such as GAPDH and POLR1A were largely unaffected, although the oncogene MYC and the Pol III transcript 5S rRNA were paradoxically increased at 5 micromolar, possibly reflecting compensatory stress responses. An rDNA promoter-driven luciferase reporter also showed reduced activity, though more modestly than at the endogenous locus, likely because the plasmid lacks native chromatin context.
Microscopy made the consequences visually unmistakable. Combining ethynyl uridine incorporation with staining for the nucleolar marker nucleolin, the team observed a significant reduction in nascent RNA synthesis from 500 nanomolar, and at 1 micromolar a prominent nucleolar ring formed by nucleolin, a classic hallmark of nucleolar stress caused by impaired Pol I transcription. Markers of nucleolar sub-compartments told a graded story: fibrillarin, marking the dense fibrillar component, showed altered distribution from 100 nanomolar, visible nucleolar caps appeared at 2 micromolar, and by 5 micromolar the nucleolus underwent complete architectural collapse. The progression from ring and cap formation to full disassembly mirrors the effects of the established Pol I inhibitor BMH-21, which the team used as a positive control.
Nucleolar stress is known to activate p53 through the impaired ribosome biogenesis checkpoint, in which free ribosomal proteins RPL5 and RPL11 bind 5S rRNA and inhibit the E3 ubiquitin ligase MDM2, thereby stabilizing p53. JP-1302 induced p53 accumulation from around 500 nanomolar, with p21 protein rising in parallel up to 2 micromolar. Silencing RPL5 and RPL11 reduced the p53 and p21 response, confirming that JP-1302 engages this canonical checkpoint. Yet at 5 micromolar the picture inverted: p21 protein and its messenger RNA both fell, even in p53-knockout cells, indicating a p53-independent mechanism of p21 depletion at high doses, consistent with the compound’s broader transcriptional suppression. Other p53 targets, ZMAT3 and MDM2, followed the same pattern.
Cell fate experiments revealed a sharp concentration threshold. At 1 micromolar, U2OS cells showed no significant death, and the effects were fully reversible after an 8-hour treatment followed by washout. At 5 micromolar, however, cells died extensively and irreversibly. EdU incorporation assays showed S-phase depletion and accumulation in G1 and G2 at low doses, and remarkably this cell-cycle arrest occurred equally in p53-wildtype and p53-knockout cells, meaning the cytostatic effect does not require p53 signalling. Mechanistically, the higher-dose regime proved far more destructive: a RADAR assay detected covalent trapping of topoisomerase II alpha and beta on DNA at 3 micromolar, chromatin fractionation showed enrichment of TOP2A, TOP2B, TOP1 and the FACT complex subunits SSRP1 and SPT16, and only at these higher concentrations did the DNA damage marker gamma-H2AX appear, delayed until 24 hours. Molecular docking and a fluorescence intercalator displacement assay supported direct DNA intercalation, though without the clear GC-content preference shown by actinomycin D and BMH-21.
The authors are candid about limitations: the non-cancerous BJ fibroblasts and RPE1 cells showed IC50 values in the same low-micromolar range as the most sensitive cancer lines, so a robust in vitro therapeutic window has not yet been demonstrated, and no reconstituted in vitro Pol I transcription assay was performed to prove direct enzyme inhibition. The upstream mechanism by which POLR1A is selectively routed to the proteasome also remains unresolved, though the E3 ligase FBXL14 is a strong candidate. Even so, the compound’s central nervous system pharmacokinetics make it especially intriguing for malignant brain tumours: all three glioblastoma lines tested, LN229, A172 and H4, showed low micromolar IC50 values, and alpha-2C-adrenergic receptors are expressed in specific brain structures and glioblastoma microenvironments including pericytes. The team suggests that chemical optimization of the acridine scaffold could yield more selective analogues, and that combining Pol I inhibition with autophagy inhibitors, a strategy known to counter pro-survival autophagy in solid tumours, may boost efficacy. For now, JP-1302 stands as a pharmacologically distinct addition to the growing arsenal of ribosome biogenesis inhibitors, one that couples rRNA synthesis shutdown with topoisomerase trapping in a single, brain-penetrant scaffold.
Subject of Research: Inhibition of RNA polymerase I transcription and nucleolar stress induction by the acridine derivative JP-1302 in cancer cell lines
Article Title: JP-1302 inhibits RNA polymerase I transcription and induces nucleolar stress in cancer cell lines
Article References: Saproo, S., Papadaki, S., Fernandez-Martinez, J., Sultana, P., Kanellis, D. C., Bartek, J., & Lindström, M. S. (2026). JP-1302 inhibits RNA polymerase I transcription and induces nucleolar stress in cancer cell lines. Cell Death Discovery, 12(1), Article 389. https://doi.org/10.1038/s41420-026-03381-8
Image Credits: AI Generated
DOI: 10.1038/s41420-026-03381-8
Keywords: JP-1302, RNA polymerase I, nucleolar stress, ribosome biogenesis, POLR1A, cancer, glioblastoma, p53, topoisomerase II, DNA intercalation, FACT complex, acridine derivatives
News Source: Nathaniel Bowman. (October 8, 2026). Brain-Penetrating Acridine Drug JP-1302 Cripples Cancer Cells by Shutting Down Ribosome Factory. Scienmag.
