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  • Perspective
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Leveraging extrachromosomal DNA to fine-tune trials of targeted therapy for glioblastoma: opportunities and challenges

Nature Reviews Clinical Oncology volume 19, pages 733–743 (2022)Cite this article

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Abstract

Glioblastoma evolution is facilitated by intratumour heterogeneity, which poses a major hurdle to effective treatment. Evidence indicates a key role for oncogene amplification on extrachromosomal DNA (ecDNA) in accelerating tumour evolution and thus resistance to treatment, particularly in glioblastomas. Oncogenes contained within ecDNA can reach high copy numbers and expression levels, and their unequal segregation can result in more rapid copy number changes in response to therapy than is possible through natural selection of intrachromosomal genomic loci. Notably, targeted therapies inhibiting oncogenic pathways have failed to improve glioblastoma outcomes. In this Perspective, we outline reasons for this disappointing lack of clinical translation and present the emerging evidence implicating ecDNA as an important driver of tumour evolution. Furthermore, we suggest that through detection of ecDNA, patient selection for clinical trials of novel agents can be optimized to include those most likely to benefit based on current understanding of resistance mechanisms. We discuss the challenges to successful translation of this approach, including accurate detection of ecDNA in tumour tissue with novel technologies, development of faithful preclinical models for predicting the efficacy of novel agents in the presence of ecDNA oncogenes, and understanding the mechanisms of ecDNA formation during cancer evolution and how they could be attenuated therapeutically. Finally, we evaluate the feasibility of routine ecDNA characterization in the clinic and how this process could be integrated with other methods of molecular stratification to maximize the potential for clinical translation of precision medicines.

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Fig. 1: Key challenges to translating targeted therapies for glioblastoma into the clinic and their intimate relationship with ecDNA.
Fig. 2: ecDNA inheritance drives intratumour genetic heterogeneity.
Fig. 3: Novel tools for ecDNA detection and characterization in glioblastoma samples.

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References

  1. Stupp, R. et al. Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. Lancet Oncol. 10, 459–466 (2009).

    Article  CAS  PubMed  Google Scholar 

  2. Touat, M., Idbaih, A., Sanson, M. & Ligon, K. L. Glioblastoma targeted therapy: updated approaches from recent biological insights. Ann. Oncol. 28, 1457–1472 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Eckel-Passow, J. E. et al. Glioma groups based on 1p/19q, IDH, and TERT promoter mutations in tumors. N. Engl. J. Med. 372, 2499–2508 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Jaunmuktane, Z. et al. Methylation array profiling of adult brain tumours: diagnostic outcomes in a large, single centre. Acta Neuropathol. Commun. 7, 24 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Capper, D. et al. DNA methylation-based classification of central nervous system tumours. Nature 555, 469–474 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Louis, D. N. et al. The 2021 WHO classification of tumors of the central nervous system: a summary. Neuro Oncol. 23, 1231–1251 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Ceccarelli, M. et al. Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma. Cell 164, 550–563 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008).

    Article  Google Scholar 

  9. Brennan, C. W. et al. The somatic genomic landscape of glioblastoma. Cell 155, 462–477 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Barthel, F. P. et al. Longitudinal molecular trajectories of diffuse glioma in adults. Nature 576, 112–120 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Verhaak, R. G. et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17, 98–110 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Wang, Q. et al. Tumor evolution of glioma-intrinsic gene expression subtypes associates with immunological changes in the microenvironment. Cancer Cell 32, 42–56 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Klughammer, J. et al. The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space. Nat. Med. 24, 1611–1624 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Hegi, M. E. et al. MGMT gene silencing and benefit from temozolomide in glioblastoma. N. Engl. J. Med. 352, 997–1003 (2005).

    Article  CAS  PubMed  Google Scholar 

  15. de Souza, C. F. et al. A distinct DNA methylation shift in a subset of glioma CpG island methylator phenotypes during tumor recurrence. Cell Rep. 23, 637–651 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Haber, D. A. & Schimke, R. T. Unstable amplification of an altered dihydrofolate reductase gene associated with double-minute chromosomes. Cell 26, 355–362 (1981).

    Article  CAS  PubMed  Google Scholar 

  17. Bigner, S. H., Friedman, H. S., Vogelstein, B., Oakes, W. J. & Bigner, D. D. Amplification of the c-myc gene in human medulloblastoma cell lines and xenografts. Cancer Res. 50, 2347–2350 (1990).

    CAS  PubMed  Google Scholar 

  18. Schwab, M. et al. Amplified DNA with limited homology to myc cellular oncogene is shared by human neuroblastoma cell lines and a neuroblastoma tumour. Nature 305, 245–248 (1983).

    Article  CAS  PubMed  Google Scholar 

  19. Turner, K. M. et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 543, 122–125 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Verhaak, R. G. W., Bafna, V. & Mischel, P. S. Extrachromosomal oncogene amplification in tumour pathogenesis and evolution. Nat. Rev. Cancer 19, 283–288 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Paulsen, T., Kumar, P., Koseoglu, M. M. & Dutta, A. Discoveries of extrachromosomal circles of DNA in normal and tumor cells. Trends Genet. 34, 270–278 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Storlazzi, C. T. et al. Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure. Genome Res. 20, 1198–1206 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kim, H. et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat. Genet. 52, 891–897 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Yi, E. et al. Live-cell imaging shows uneven segregation of extrachromosomal DNA elements and transcriptionally active extrachromosomal DNA hubs in cancer. Cancer Disco. 12, 468–483 (2021).

    Article  Google Scholar 

  25. Wu, S. et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 575, 699–703 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Hung, K. L. et al. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature 600, 731–736 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Nathanson, D. A. et al. Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science 343, 72–76 (2014).

    Article  CAS  PubMed  Google Scholar 

  28. deCarvalho, A. C. et al. Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma. Nat. Genet. 50, 708–717 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. White, K. et al. New hints towards a precision medicine strategy for IDH wild-type glioblastoma. Ann. Oncol. 31, 1679–1692 (2020).

    Article  CAS  PubMed  Google Scholar 

  30. Zhao, H. F. et al. Recent advances in the use of PI3K inhibitors for glioblastoma multiforme: current preclinical and clinical development. Mol. Cancer 16, 100 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  31. Liu, E. K., Sulman, E. P., Wen, P. Y. & Kurz, S. C. Novel therapies for glioblastoma. Curr. Neurol. Neurosci. Rep. 20, 19 (2020).

    Article  PubMed  Google Scholar 

  32. Dresemann, G. et al. Imatinib in combination with hydroxyurea versus hydroxyurea alone as oral therapy in patients with progressive pretreated glioblastoma resistant to standard dose temozolomide. J. Neurooncol. 96, 393–402 (2010).

    Article  CAS  PubMed  Google Scholar 

  33. Wick, W. et al. Phase III study of enzastaurin compared with lomustine in the treatment of recurrent intracranial glioblastoma. J. Clin. Oncol. 28, 1168–1174 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Ma, D. J. et al. A phase II trial of everolimus, temozolomide, and radiotherapy in patients with newly diagnosed glioblastoma: NCCTG N057K. Neuro Oncol. 17, 1261–1269 (2015).

    Article  CAS  PubMed  Google Scholar 

  35. Westphal, M. et al. A randomised, open label phase III trial with nimotuzumab, an anti-epidermal growth factor receptor monoclonal antibody in the treatment of newly diagnosed adult glioblastoma. Eur. J. Cancer 51, 522–532 (2015).

    Article  CAS  PubMed  Google Scholar 

  36. Reardon, D. A. et al. Phase I/randomized phase II study of afatinib, an irreversible ErbB family blocker, with or without protracted temozolomide in adults with recurrent glioblastoma. Neuro Oncol. 17, 430–439 (2015).

    CAS  PubMed  Google Scholar 

  37. Westphal, M., Maire, C. L. & Lamszus, K. EGFR as a target for glioblastoma treatment: an unfulfilled promise. CNS Drugs 31, 723–735 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Seystahl, K., Wick, W. & Weller, M. Therapeutic options in recurrent glioblastoma – an update. Crit. Rev. Oncol. Hematol. 99, 389–408 (2016).

    Article  PubMed  Google Scholar 

  39. Weenink, B., French, P. J., Sillevis Smitt, P. A. E., Debets, R. & Geurts, M. Immunotherapy in glioblastoma: current shortcomings and future perspectives. Cancers 12, 751 (2020).

    Article  CAS  PubMed Central  Google Scholar 

  40. Mellinghoff, I. K. et al. Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N. Engl. J. Med. 353, 2012–2024 (2005).

    Article  CAS  PubMed  Google Scholar 

  41. Vivanco, I. et al. Differential sensitivity of glioma- versus lung cancer-specific EGFR mutations to EGFR kinase inhibitors. Cancer Discov. 2, 458–471 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Favero, F. et al. Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome. Ann. Oncol. 26, 880–887 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Francis, J. M. et al. EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing. Cancer Discov. 4, 956–971 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Meyer, M. et al. Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity. Proc. Natl Acad. Sci. USA 112, 851–856 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Qazi, M. A. et al. Intratumoral heterogeneity: pathways to treatment resistance and relapse in human glioblastoma. Ann. Oncol. 28, 1448–1456 (2017).

    Article  CAS  PubMed  Google Scholar 

  46. Dagogo-Jack, I. & Shaw, A. T. Tumour heterogeneity and resistance to cancer therapies. Nat. Rev. Clin. Oncol. 15, 81–94 (2018).

    Article  CAS  PubMed  Google Scholar 

  47. Akhavan, D. et al. De-repression of PDGFRβ transcription promotes acquired resistance to EGFR tyrosine kinase inhibitors in glioblastoma patients. Cancer Discov. 3, 534–547 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Yeo, A. T. et al. EGFRvIII tumorigenicity requires PDGFRA co-signaling and reveals therapeutic vulnerabilities in glioblastoma. Oncogene 40, 2682–2696 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Snuderl, M. et al. Mosaic amplification of multiple receptor tyrosine kinase genes in glioblastoma. Cancer Cell 20, 810–817 (2011).

    Article  CAS  PubMed  Google Scholar 

  50. Mai, W. X. et al. Cytoplasmic p53 couples oncogene-driven glucose metabolism to apoptosis and is a therapeutic target in glioblastoma. Nat. Med. 23, 1342–1351 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Wei, W. et al. Single-cell phosphoproteomics resolves adaptive signaling dynamics and informs targeted combination therapy in glioblastoma. Cancer Cell 29, 563–573 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Lee, J. K. et al. Spatiotemporal genomic architecture informs precision oncology in glioblastoma. Nat. Genet. 49, 594–599 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Tan, S. K. et al. Drug repositioning in glioblastoma: a pathway perspective. Front. Pharmacol. 9, 218 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  54. Hammarlund-Udenaes, M., Friden, M., Syvanen, S. & Gupta, A. On the rate and extent of drug delivery to the brain. Pharm. Res. 25, 1737–1750 (2008).

    Article  CAS  PubMed  Google Scholar 

  55. Bagley, S. J. et al. Glioblastoma clinical trials: current landscape and opportunities for improvement. Clin. Cancer Res. 28, 594–602 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  56. Vogelbaum, M. A. et al. Phase 0 and window of opportunity clinical trial design in neuro-oncology: a RANO review. Neuro Oncol. 22, 1568–1579 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  57. Daneman, R., Zhou, L., Kebede, A. A. & Barres, B. A. Pericytes are required for blood-brain barrier integrity during embryogenesis. Nature 468, 562–566 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Abbott, N. J., Ronnback, L. & Hansson, E. Astrocyte-endothelial interactions at the blood-brain barrier. Nat. Rev. Neurosci. 7, 41–53 (2006).

    Article  CAS  PubMed  Google Scholar 

  59. He, Q. et al. Towards improvements for penetrating the blood-brain barrier–recent progress from a material and pharmaceutical perspective. Cells 7, 24 (2018).

    Article  PubMed Central  Google Scholar 

  60. Banks, W. A. From blood-brain barrier to blood-brain interface: new opportunities for CNS drug delivery. Nat. Rev. Drug Discov. 15, 275–292 (2016).

    Article  CAS  PubMed  Google Scholar 

  61. Duman, C. et al. Acyl-CoA-binding protein drives glioblastoma tumorigenesis by sustaining fatty acid oxidation. Cell Metab. 30, 274–289 (2019).

    Article  CAS  PubMed  Google Scholar 

  62. Villa, G. R. et al. An LXR-cholesterol axis creates a metabolic co-dependency for brain cancers. Cancer Cell 30, 683–693 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Bi, J. et al. Oncogene amplification in growth factor signaling pathways renders cancers dependent on membrane lipid remodeling. Cell Metab. 30, 525–538 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Bi, J. et al. Altered cellular metabolism in gliomas–an emerging landscape of actionable co-dependency targets. Nat. Rev. Cancer 20, 57–70 (2020).

    Article  CAS  PubMed  Google Scholar 

  65. Hara, T. et al. Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma. Cancer Cell 39, 779–792 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Broekman, M. L. et al. Multidimensional communication in the microenvirons of glioblastoma. Nat. Rev. Neurol. 14, 482–495 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  67. Nduom, E. K., Weller, M. & Heimberger, A. B. Immunosuppressive mechanisms in glioblastoma. Neuro Oncol. 17, vii9–vii14 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Noorani, I. et al. Novel association between microglia and stem cells in human gliomas: a contributor to tumour proliferation? J. Pathol. Clin. Res. 1, 67–75 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Cox, D., Yuncken, C. & Spriggs, A. I. Minute chromatin bodies in malignant tumours of childhood. Lancet 1, 55–58 (1965).

    Article  CAS  PubMed  Google Scholar 

  70. Levan, A. & Levan, G. Have double minutes functioning centromeres? Hereditas 88, 81–92 (1978).

    Article  CAS  PubMed  Google Scholar 

  71. Kaufman, R. J., Brown, P. C. & Schimke, R. T. Amplified dihydrofolate reductase genes in unstably methotrexate-resistant cells are associated with double minute chromosomes. Proc. Natl Acad. Sci. USA 76, 5669–5673 (1979).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Kumar, P. et al. ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines. Sci. Adv. 6, eaba2489 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Shoshani, O. et al. Chromothripsis drives the evolution of gene amplification in cancer. Nature 591, 137–141 (2021).

    Article  CAS  PubMed  Google Scholar 

  74. Ly, P. et al. Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Nat. Genet. 51, 705–715 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Shimizu, N. et al. Generation and maintenance of acentric stable double minutes from chromosome arms in inter-species hybrid cells. BMC Mol. Cell Biol. 20, 2 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  76. Shimizu, N., Miura, Y., Sakamoto, Y. & Tsutsui, K. Plasmids with a mammalian replication origin and a matrix attachment region initiate the event similar to gene amplification. Cancer Res. 61, 6987–6990 (2001).

    CAS  PubMed  Google Scholar 

  77. Wahl, G. M. The importance of circular DNA in mammalian gene amplification. Cancer Res. 49, 1333–1340 (1989).

    CAS  PubMed  Google Scholar 

  78. Wu, S., Bafna, V. & Mischel, P. S. Extrachromosomal DNA (ecDNA) in cancer pathogenesis. Curr. Opin. Genet. Dev. 66, 78–82 (2021).

    Article  CAS  PubMed  Google Scholar 

  79. Shimizu, N. Gene amplification and the extrachromosomal circular DNA. Genes 12, 1533 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Kanda, T., Otter, M. & Wahl, G. M. Mitotic segregation of viral and cellular acentric extrachromosomal molecules by chromosome tethering. J. Cell Sci. 114, 49–58 (2001).

    Article  CAS  PubMed  Google Scholar 

  81. Tanaka, T. & Shimizu, N. Induced detachment of acentric chromatin from mitotic chromosomes leads to their cytoplasmic localization at G(1) and the micronucleation by lamin reorganization at S phase. J. Cell Sci. 113, 697–707 (2000).

    Article  CAS  PubMed  Google Scholar 

  82. Lundberg, G. et al. Binomial mitotic segregation of MYCN-carrying double minutes in neuroblastoma illustrates the role of randomness in oncogene amplification. PLoS ONE 3, e3099 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  83. Lange, J. T. et al. Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers. Preprint at bioRxiv https://doi.org/10.1101/2021.06.11.447968 (2021).

    Article  Google Scholar 

  84. Vogt, N. et al. Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma. Nucleic Acids Res. 42, 13194–13205 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Bergstrom, E. N. et al. Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. Nature 602, 510–517 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Zhu, B. et al. Mutations in the HPV16 genome induced by APOBEC3 are associated with viral clearance. Nat. Commun. 11, 886 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Pichugin, Y., Huang, W. & Werner, B. Stochastic dynamics of extra-chromosomal DNA. Preprint at bioRxiv https://doi.org/10.1101/2019.12.15.876714 (2019).

    Article  Google Scholar 

  88. Shimizu, N., Kanda, T. & Wahl, G. M. Selective capture of acentric fragments by micronuclei provides a rapid method for purifying extrachromosomally amplified DNA. Nat. Genet. 12, 65–71 (1996).

    Article  CAS  PubMed  Google Scholar 

  89. Valent, A. et al. In vivo elimination of acentric double minutes containing amplified MYCN from neuroblastoma tumor cells through the formation of micronuclei. Am. J. Pathol. 158, 1579–1584 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Kneissig, M. et al. Micronuclei-based model system reveals functional consequences of chromothripsis in human cells. Elife 8, e50292 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  91. Oobatake, Y. & Shimizu, N. Double-strand breakage in the extrachromosomal double minutes triggers their aggregation in the nucleus, micronucleation, and morphological transformation. Genes. Chromosomes Cancer 59, 133–143 (2020).

    Article  CAS  PubMed  Google Scholar 

  92. Sanchez, A. M., Barrett, J. T. & Schoenlein, P. V. Fractionated ionizing radiation accelerates loss of amplified MDR1 genes harbored by extrachromosomal DNA in tumor cells. Cancer Res. 58, 3845–3854 (1998).

    CAS  PubMed  Google Scholar 

  93. Schoenlein, P. V. et al. Radiation therapy depletes extrachromosomally amplified drug resistance genes and oncogenes from tumor cells via micronuclear capture of episomes and double minute chromosomes. Int. J. Radiat. Oncol. Biol. Phys. 55, 1051–1065 (2003).

    Article  CAS  PubMed  Google Scholar 

  94. Eckhardt, S. G. et al. Induction of differentiation in HL60 cells by the reduction of extrachromosomally amplified c-myc. Proc. Natl Acad. Sci. USA 91, 6674–6678 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Shimizu, N. et al. Loss of amplified c-myc genes in the spontaneously differentiated HL-60 cells. Cancer Res. 54, 3561–3567 (1994).

    CAS  PubMed  Google Scholar 

  96. Shimizu, N., Ochi, T. & Itonaga, K. Replication timing of amplified genetic regions relates to intranuclear localization but not to genetic activity or G/R band. Exp. Cell Res. 268, 201–210 (2001).

    Article  CAS  PubMed  Google Scholar 

  97. Mitsuda, S. H. & Shimizu, N. Epigenetic repeat-induced gene silencing in the chromosomal and extrachromosomal contexts in human cells. PLoS ONE 11, e0161288 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  98. Smith, G. et al. c-Myc-induced extrachromosomal elements carry active chromatin. Neoplasia 5, 110–120 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Helmsauer, K. et al. Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma. Nat. Commun. 11, 5823 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Morton, A. R. et al. Functional enhancers shape extrachromosomal oncogene amplifications. Cell 179, 1330–1341 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Zhu, Y. et al. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell 39, 694–707 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Rajkumar, U. et al. EcSeg: semantic segmentation of metaphase images containing extrachromosomal DNA. iScience 21, 428–435 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Deshpande, V. et al. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat. Commun. 10, 392 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Luebeck, J. et al. AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications. Nat. Commun. 11, 4374 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Shale, C. et al. Unscrambling cancer genomes via integrated analysis of structural variation and copy number. Cell Genomics 2, 100112 (2022).

    Article  CAS  Google Scholar 

  106. Prada-Luengo, I., Krogh, A., Maretty, L. & Regenberg, B. Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads. BMC Bioinforma. 20, 663 (2019).

    Article  CAS  Google Scholar 

  107. Moller, H. D., Parsons, L., Jorgensen, T. S., Botstein, D. & Regenberg, B. Extrachromosomal circular DNA is common in yeast. Proc. Natl Acad. Sci. USA 112, E3114–E3122 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  108. Koche, R. P. et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat. Genet. 52, 29–34 (2020).

    Article  CAS  PubMed  Google Scholar 

  109. Wang, Y. et al. eccDNAs are apoptotic products with high innate immunostimulatory activity. Nature 599, 308–314 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Hung, K. L. et al. Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH. Preprint at bioRxiv https://doi.org/10.1101/2021.11.28.470285 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  111. Alitalo, K., Schwab, M., Lin, C. C., Varmus, H. E. & Bishop, J. M. Homogeneously staining chromosomal regions contain amplified copies of an abundantly expressed cellular oncogene (c-myc) in malignant neuroendocrine cells from a human colon carcinoma. Proc. Natl Acad. Sci. USA 80, 1707–1711 (1983).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. LeBlanc, V. G. et al. Single-cell landscapes of primary glioblastomas and matched explants and cell lines show variable retention of inter- and intratumor heterogeneity. Cancer Cell 40, 379–392 (2022).

    Article  CAS  PubMed  Google Scholar 

  113. Shen, Y. et al. Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments. Proc. Natl Acad. Sci. USA 116, 19098–19108 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Noorani, I. Genetically engineered mouse models of gliomas: technological developments for translational discoveries. Cancers 11, 1335 (2019).

    Article  CAS  PubMed Central  Google Scholar 

  115. Haddad, A. F. et al. Mouse models of glioblastoma for the evaluation of novel therapeutic strategies. Neurooncol Adv. 3, vdab100 (2021).

    PubMed  PubMed Central  Google Scholar 

  116. Chen, J., McKay, R. M. & Parada, L. F. Malignant glioma: lessons from genomics, mouse models, and stem cells. Cell 149, 36–47 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Noorani, I. et al. PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas. Genome Biol. 21, 181 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Noorani, I., Bradley, A. & de la Rosa, J. CRISPR and transposon in vivo screens for cancer drivers and therapeutic targets. Genome Biol. 21, 204 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  119. Alcantara Llaguno, S. et al. Cell-of-origin susceptibility to glioblastoma formation declines with neural lineage restriction. Nat. Neurosci. 22, 545–555 (2019).

    Article  PubMed  Google Scholar 

  120. Zou, H. et al. Double minute amplification of mutant PDGF receptor α in a mouse glioma model. Sci. Rep. 5, 8468 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Yan, C. T. et al. XRCC4 suppresses medulloblastomas with recurrent translocations in p53-deficient mice. Proc. Natl Acad. Sci. USA 103, 7378–7383 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Smolen, G. A. et al. Frequent Met oncogene amplification in a Brca1/Trp53 mouse model of mammary tumorigenesis. Cancer Res. 66, 3452–3455 (2006).

    Article  CAS  PubMed  Google Scholar 

  123. Wu, T. et al. Extrachromosomal DNA formation enables tumor immune escape potentially through regulating antigen presentation gene expression. Sci. Rep. 12, 3590 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Ye, L. et al. In vivo CRISPR screening in CD8 T cells with AAV-Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma. Nat. Biotechnol. 37, 1302–1313 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Koga, T. et al. Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells. Nat. Commun. 11, 550 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Jacob, F., Ming, G. L. & Song, H. Generation and biobanking of patient-derived glioblastoma organoids and their application in CAR T cell testing. Nat. Protoc. 15, 4000–4033 (2020).

    Article  CAS  PubMed  Google Scholar 

  127. Jacob, F. et al. A patient-derived glioblastoma organoid model and biobank recapitulates inter- and intra-tumoral heterogeneity. Cell 180, 188–204 (2020).

    Article  CAS  PubMed  Google Scholar 

  128. Neufeld, L. et al. Microengineered perfusable 3D-bioprinted glioblastoma model for in vivo mimicry of tumor microenvironment. Sci. Adv. 7, eabi9119 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Chaligne, R. et al. Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states. Nat. Genet. 53, 1469–1479 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Rao, A., Barkley, D., Franca, G. S. & Yanai, I. Exploring tissue architecture using spatial transcriptomics. Nature 596, 211–220 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Hyman, D. M. et al. Vemurafenib in multiple nonmelanoma cancers with BRAF V600 mutations. N. Engl. J. Med. 373, 726–736 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Moller, H. D. et al. CRISPR-C: circularization of genes and chromosome by CRISPR in human cells. Nucleic Acids Res. 46, e131 (2018).

    PubMed  PubMed Central  Google Scholar 

  133. Song, K. et al. Plasticity of extrachromosomal and intrachromosomal BRAF amplifications in overcoming targeted therapy dosage challenges. Cancer Discov. 12, 1046–1069 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Gregory, J. V. et al. Systemic brain tumor delivery of synthetic protein nanoparticles for glioblastoma therapy. Nat. Commun. 11, 5687 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Oberoi, R. K. et al. Strategies to improve delivery of anticancer drugs across the blood-brain barrier to treat glioblastoma. Neuro Oncol. 18, 27–36 (2016).

    Article  CAS  PubMed  Google Scholar 

  136. Lassman, A. B. et al. Phase 2 trial of dasatinib in target-selected patients with recurrent glioblastoma (RTOG 0627). Neuro Oncol. 17, 992–998 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Cescon, D. W., Bratman, S. V., Chan, S. M. & Siu, L. L. Circulating tumor DNA and liquid biopsy in oncology. Nat. Cancer 1, 276–290 (2020).

    Article  CAS  PubMed  Google Scholar 

  138. Zhu, J. et al. Molecular characterization of cell-free eccDNAs in human plasma. Sci. Rep. 7, 10968 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  139. Von Hoff, D. D. et al. Hydroxyurea accelerates loss of extrachromosomally amplified genes from tumor cells. Cancer Res. 51, 6273–6279 (1991).

    Google Scholar 

  140. Prochazka, P., Hrabeta, J., Vicha, A. & Eckschlager, T. Expulsion of amplified MYCN from homogenously staining chromosomal regions in neuroblastoma cell lines after cultivation with cisplatin, doxorubicin, hydroxyurea, and vincristine. Cancer Genet. Cytogenet. 196, 96–104 (2010).

    Article  CAS  PubMed  Google Scholar 

  141. Yu, L. et al. Gemcitabine eliminates double minute chromosomes from human ovarian cancer cells. PLoS ONE 8, e71988 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Watkins, T. B. K. et al. Pervasive chromosomal instability and karyotype order in tumour evolution. Nature 587, 126–132 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Lopez, S. et al. Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution. Nat. Genet. 52, 283–293 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The work of I.N. is funded by an NIHR Clinical Lectureship, the UCL Biomedical Research Centre and the Academy of Medical Sciences. P.S.M. leads the Cancer Grand Challenges eDyNAmiC team, with support from Cancer Research UK and the US NIH National Cancer Institute (NCI); his work is also supported by NCI grant RO1CA238249, and The National Brain Tumor Society. C.S. is a Royal Society Napier Research Professor. The work of I.N. and C.S. is supported by The Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001169), the UK Medical Research Council (FC001169) and the Wellcome Trust (FC001169). The authors thank C. Weeden for her critical review and comments on the manuscript.

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Authors and Affiliations

  1. Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK

    Imran Noorani & Charles Swanton

  2. Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UK

    Imran Noorani

  3. Department of Pathology, Stanford University School of Medicine and Sarafan ChEM-H, Stanford University, Stanford, CA, USA

    Paul S. Mischel

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The authors contributed equally to all aspects of the article.

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Correspondence to Imran Noorani, Paul S. Mischel or Charles Swanton.

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Competing interests

P.S.M. is a co-founder of Boundless Bio, a company focused on developing new treatments for patients with ecDNA-driven cancers; he has equity in the company and chairs the scientific advisory board, for which he is compensated. C.S. has received grant funding from AstraZeneca, Boehringer Ingelheim, Bristol Myers Squibb, Invitae (previously ArcherDx), Ono Pharmaceutical, Pfizer and Roche/Ventana Medical Systems. C.S. is an advisory board member for AstraZeneca and Chief Investigator of the AstraZeneca MERMAID-1 and MERMAID-2 clinical trials, and is also Chief Investigator of the NHS-Galleri trial sponsored by GRAIL. C.S. has consulted for Achilles Therapeutics, Amgen, AstraZeneca, Bicycle Therapeutics, Bristol Myers Squibb, Genentech, GRAIL, GSK, Illumina, Medicxi, Metabomed, MSD, Novartis, Pfizer, Roche Innovation Centre Shanghai, Roche/Ventana Medical Systems, and the Sarah Cannon Research Institute. C.S. held stock options in Apogen Biotechnologies and GRAIL until June 2021, currently has stock options in Bicycle Therapeutics and Epic Bioscience, and has stock options and is a co-founder of Achilles Therapeutics. I.N. declares no competing interests.

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Nature Reviews Clinical Oncology thanks B. Regenberg, who co-reviewed with J. B. Noer; N. Shimizu; R. Verhaak and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Noorani, I., Mischel, P.S. & Swanton, C. Leveraging extrachromosomal DNA to fine-tune trials of targeted therapy for glioblastoma: opportunities and challenges. Nat Rev Clin Oncol 19, 733–743 (2022). https://doi.org/10.1038/s41571-022-00679-1

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