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Cited by 7Genomics and Chromatin DynamicsGlioma Diagnosis and TreatmentChromatin Remodeling and Cancer

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Synthetic ZFTA fusions pinpoint disordered protein domain acquisition as a mechanism of brain tumorigenesis

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Arabzade, A., Shirnekhi, H. K., Varadharajan, S., Ippagunta, S. M., Phillips, A. H., Laboe, N., Baggett, D. W., Wahiduzzaman, Jo, M., Zheng, T., Pathak, R., Gee, D., Bhimsaria, D., Wu, H., Gao, X., Liu, J., Emanus, E., Bland, A., Kardian, A., Hancock, A., Holcomb, B., Wright, T., Bugbee, T., Sun, H., Zhai, M., Caesar, E., Park, M., Tripathi, S., Shirinifard, A., Lowe, K., Khalighifar, A., Petersen, R. A., King, S., Stabley, D., Pitre, A., Campbell, G. E., Park, C-G, Freyaldenhoven, W. T., Chandra, B., Xia, Y., Bonten, E., Achari, A., Kandikonda, S., Carisey, A., Pounds, S. B., Xu, J., Ellison, D. W., Deneen, B., Bertrand, K. C., Kriwacki, R. W., Mack, S. C.·2025·Nature Cell Biology
DOI 10.1038/s41556-025-01745-3PMC PMC12431856

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Abstract

Over 95% of ependymomas that arise in the cortex are driven by a gene fusion involving the zinc finger translocation-associated (ZFTA) protein. Here, using super-resolution and lattice light-sheet microscopy, we demonstrate that the most frequent fusion variant, ZFTA–RELA (ZR), forms dynamic nuclear condensates that are required for oncogene expression and tumorigenesis. Mutagenesis studies of ZR reveal a key intrinsically disordered region (IDR) in RELA that governs condensate formation. Condensate-modulating IDR mutations introduced into ZR impaired its genomic occupancy at oncogenic loci and inhibited the recruitment of transcriptional effector proteins, such as MED1, BRD4 and RNA polymerase II. Using nuclear magnetic resonance spectroscopy, we examined the DNA-binding residues of the critical zinc finger (ZF1) found in ZR and characterized their significance for condensate formation, genomic binding and oncogene activation. We generated synthetic ZFTA fusion proteins where IDRs from known condensate-forming proteins were grafted into ZR. Synthetic ZFTA fusion oncoproteins utilizing IDRs from EWS and FUS restored condensate formation, oncogene transcription and tumour initiation in mice. These findings provide key insights into the oncogenic mechanism of ZR and the importance of IDR acquisition in fusion oncoproteins in brain cancer.

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  1. Pajtler, K. W. et al. The current consensus on the clinical management of intracranial ependymoma and its distinct molecular variants. Acta Neuropathol. 133, 5–12 (2017). · DOI
  2. Hwang, E. I., Hanson, D., Filbin, M. G. & Mack, S. C. Why haven’t we solved intracranial pediatric ependymoma? Current questions and barriers to treatment advances. Neoplasia 39, 100895 (2023). · DOI
  3. Saleh, A. H. et al. The biology of ependymomas and emerging novel therapies. Nat. Rev. Cancer 22, 208–222 (2022). · DOI
  4. Arabzade, A. et al. ZFTA–RELA dictates oncogenic transcriptional programs to drive aggressive supratentorial ependymoma. Cancer Discov. 11, 2200–2215 (2021). · DOI
  5. Kupp, R. et al. ZFTA translocations constitute ependymoma chromatin remodeling and transcription factors. Cancer Discov. 11, 2216–2229 (2021). · DOI
  6. Ozawa, T. et al. A de novo mouse model of C11orf95–RELA fusion-driven ependymoma identifies driver functions in addition to NF-κB. Cell Rep. 23, 3787–3797 (2018). · DOI
  7. Zheng, T. et al. Cross-species genomics reveals oncogenic dependencies in ZFTA/C11orf95 fusion-positive supratentorial ependymomas. Cancer Discov. 11, 2230–2247 (2021). · DOI
  8. Parker, M. et al. C11orf95–RELA fusions drive oncogenic NF-κB signalling in ependymoma. Nature 506, 451–455 (2014). · DOI
  9. Herranz-Pérez, V. et al. Ependymoma associated protein Zfta is expressed in immature ependymal cells but is not essential for ependymal development in mice. Sci. Rep. 12, 1493 (2022). · DOI
  10. Mitrea, D. M. & Kriwacki, R. W. Phase separation in biology; functional organization of a higher order. Cell Commun. Signal 14, 1 (2016). · DOI
  11. Banani, S. F., Lee, H. O., Hyman, A. A. & Rosen, M. K. Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18, 285–298 (2017). · DOI
  12. Ahn, J. H. et al. Phase separation drives aberrant chromatin looping and cancer development. Nature 595, 591–595 (2021). · DOI
  13. Chandra, B. et al. Phase separation mediates NUP98 fusion oncoprotein leukemic transformation. Cancer Discov. https://doi.org/10.1158/2159-8290.CD-21-0674 (2021). · DOI
  14. Boulay, G. et al. Cancer-specific retargeting of BAF complexes by a prion-like domain. Cell 171, 163–178 (2017). · DOI
  15. Terlecki-Zaniewicz, S. et al. Biomolecular condensation of NUP98 fusion proteins drives leukemogenic gene expression. Nat. Struct. Mol. Biol. 28, 190–201 (2021). · DOI
  16. Qin, Z. et al. Phase separation of EML4–ALK in firing downstream signaling and promoting lung tumorigenesis. Cell Discov. 7, 33 (2021). · DOI
  17. Shirnekhi, H. K., Chandra, B. & Kriwacki, R. The role of phase-separated condensates in fusion oncoprotein–driven cancers. Annu. Rev. Cancer Biol. 7, 73–91 (2023). · DOI
  18. Zuo, L. et al. Loci-specific phase separation of FET fusion oncoproteins promotes gene transcription. Nat. Commun. 12, 1491 (2021). · DOI
  19. Chong, S. et al. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science https://doi.org/10.1126/science.aar2555 (2018). · DOI · Paper page
  20. Feric, M. et al. Coexisting liquid phases underlie nucleolar subcompartments. Cell 165, 1686–1697 (2016). · DOI
  21. Mack, S. C. et al. Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling. Nature 553, 101–105 (2018). · DOI
  22. Tripathi, S. et al. Defining the condensate landscape of fusion oncoproteins. Nat. Commun. https://doi.org/10.1038/s41467-023-41655-2 (2023). · DOI
  23. Chen, H. C. et al. Histone serotonylation regulates ependymoma tumorigenesis. Nature 632, 903–910 (2024). · DOI
  24. Chen, F. E., Huang, D. B., Chen, Y. Q. & Ghosh, G. Crystal structure of p50/p65 heterodimer of transcription factor NF-κB bound to DNA. Nature 391, 410–413 (1998). · DOI
  25. Bhimsaria, D. et al. Specificity landscapes unmask submaximal binding site preferences of transcription factors. Proc. Natl Acad. Sci. USA 115, E10586–e10595 (2018). · DOI
  26. Lee, M. S., Gippert, G. P., Soman, K. V., Case, D. A. & Wright, P. E. Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 245, 635–637 (1989). · DOI
  27. Hu, X. et al. Nuclear condensates of YAP fusion proteins alter transcription to drive ependymoma tumourigenesis. Nat. Cell Biol. 25, 323–336 (2023).
  28. Wang, Y. et al. Dissolution of oncofusion transcription factor condensates for cancer therapy. Nat. Chem. Biol. 19, 1223–1234 (2023). · DOI
  29. Cai, D. et al. Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression. Nat. Cell Biol. 21, 1578–1589 (2019). · DOI
  30. Klein, I. A. et al. Partitioning of cancer therapeutics in nuclear condensates. Science 368, 1386–1392 (2020). · DOI
  31. Kilgore, H. R. et al. Distinct chemical environments in biomolecular condensates. Nat. Chem. Biol. https://doi.org/10.1038/s41589-023-01432-0 (2023). · DOI
  32. Ambadi Thody, S. et al. Small-molecule properties define partitioning into biomolecular condensates. Nat. Chem. 16, 1794–1802 (2024). · DOI
  33. Kilgore, H. R. et al. Distinct chemical environments in biomolecular condensates. Nat. Chem. Biol. 20, 291–301 (2024). · DOI
  34. Riggi, N. et al. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell 26, 668–681 (2014). · DOI
  35. Wei, M. T. et al. Nucleated transcriptional condensates amplify gene expression. Nat. Cell Biol. 22, 1187–1196 (2020). · DOI
  36. Liu, G. et al. Characterization, comparison, and optimization of lattice light sheets. Sci. Adv. 9, eade6623 (2023). · DOI
  37. Shi, Y., Daugird, T. A. & Legant, W. R. A quantitative analysis of various patterns applied in lattice light sheet microscopy. Nat. Commun. 13, 4607 (2022). · DOI
  38. Ahrens, J., Geveci, B. & Law, C. in Visualization Handbook (eds Hansen C. D. & Johnson C. R.) 717–731 (Butterworth-Heinemann, 2005). · DOI
  39. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012). · DOI · Paper page
  40. Kay, L. E., Xu, G. Y. & Yamazaki, T. Enhanced-sensitivity triple-resonance spectroscopy with minimal H2O saturation. J. Magn. Reson. A 109, 129–133 (1994). · DOI
  41. Muhandiram, D. R. & Kay, L. E. Gradient-enhanced triple-resonance three-dimensional NMR experiments with improved sensitivity. J. Magn. Reson. B 103, 203–216 (1994). · DOI
  42. Grzesiek, S. & Bax, A. Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins. J. Biomol. NMR 3, 185–204 (1993). · DOI
  43. Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995). · DOI
  44. Lee, W., Tonelli, M. & Markley, J. L. NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31, 1325–1327 (2015). · DOI
  45. Lee, W. et al. I-PINE web server: an integrative probabilistic NMR assignment system for proteins. J. Biomol. NMR 73, 213–222 (2019). · DOI
  46. Hafsa, N. E., Arndt, D. & Wishart, D. S. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts. Nucleic Acids Res. 43, W370–W377 (2015). · DOI
  47. Heinig, M. & Frishman, D. STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res. 32, W500–W502 (2004). · DOI · Paper page
  48. Scholz, J., Besir, H., Strasser, C. & Suppmann, S. A new method to customize protein expression vectors for fast, efficient and background free parallel cloning. BMC Biotechnol. 13, 12 (2013). · DOI

Metadata

Authors
Arabzade, A., Shirnekhi, H. K., Varadharajan, S., Ippagunta, S. M., Phillips, A. H., Laboe, N., Baggett, D. W., Wahiduzzaman, Jo, M., Zheng, T., Pathak, R., Gee, D., Bhimsaria, D., Wu, H., Gao, X., Liu, J., Emanus, E., Bland, A., Kardian, A., Hancock, A., Holcomb, B., Wright, T., Bugbee, T., Sun, H., Zhai, M., Caesar, E., Park, M., Tripathi, S., Shirinifard, A., Lowe, K., Khalighifar, A., Petersen, R. A., King, S., Stabley, D., Pitre, A., Campbell, G. E., Park, C.-G., Freyaldenhoven, W. T., Chandra, B., Xia, Y., Bonten, E., Achari, A., Kandikonda, S., Carisey, A., Pounds, S. B., Xu, J., Ellison, D. W., Deneen, B., Bertrand, K. C., Kriwacki, R. W., & Mack, S. C.
Affiliations
  • St. Jude Children's Research Hospital (US)
  • Indian Institute of Technology Roorkee (IN)
  • Baylor College of Medicine (US)
Corresponding author
  • Kriwacki, R. W.
  • Mack, S. C.
ORCID
Venue
Nature Cell Biology
Publisher
Springer Science and Business Media LLC
Published
2025-08-27
Volume
27
Issue
9
Pages
1496-1509
ISSN
  • 1465-7392 (ISSN-L)
  • 1476-4679
DOI
10.1038/s41556-025-01745-3
PMC
PMC12431856
OpenAlex
W4413740186
Cited by
7
References
1
Citations by year
2026: 7
FWCI
2.10
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Cell Biology (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • Digital Commons-TMC (Texas Medical Center) (submittedVersion)
Funders
  • U.S. Department of Health & Human Services | NIH | National Cancer Institute (P30 CA021765, R01CA284455, R01CA280203, U01CA281823, U01CA294103, R01CA246125, U54CA243124)
  • Alex's Lemonade Stand Foundation for Childhood Cancer (A Award (Mack))
  • U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (R01NS128184)
  • U.S. Department of Defense (CA220510, CA220247)
  • National Brain Tumor Society ((Mack))
  • American Lebanese Syrian Associated Charities ((Mack))
  • CERN Foundation, Robert Connor Dawes Foundation
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Health Sciences › Medicine › Oncology › Glioma Diagnosis and Treatment
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords
ependymoma, intrinsically disordered regions, nuclear condensates, fusion oncoproteins, brain tumorigenesis, RelA, DNA-binding residues, oncogene activation, MED1, BRD4, RNA polymerase II
MeSH terms
Protein Domains, Animals, Brain Neoplasms, Humans, Transcription Factors, Oncogene Proteins, Fusion, Gene Expression Regulation, Neoplastic, Zinc Fingers, RNA-Binding Protein FUS, RNA-Binding Protein EWS, Cell Line, Tumor, Mice, Transcription Factor RelA, Carcinogenesis, Intrinsically Disordered Proteins

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