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Cellular and Molecular Biology

Novel strategy to target glioblastoma-initiating cells using a braintropic adeno-associated virus carrying a miR-dependent genome-editing system

Abstract

Background

Since glioblastoma (GBM)-initiating cells (GICs) were identified as the cells-of-origin for GBM, various GIC factors have been analyzed as potential therapeutic targets. However, these targets are also present in normal cells outside of the brain, raising concerns about potential side effects when directly targeted. The aim of this study is to develop a novel method that specifically eradicates GICs with reducing side effects.

Methods

We selected micoRNAs (miRs) that are significantly decreased in GICs compared to normal cells and developed a genome-editing (GE) system that knocks out a functional GIC factor in a miR-dependent manner (miR-dependent GE). Additionally, we developed mosaic-capsids that consist of braintropic and universal capsids, which deliver genes into GIC brain tumors.

Results

Systemic administration of the mosaic-capsids Adeno-associated virus (AAV) carrying a miR-dependent GFP expression cassette selectively expressed GFP in GICs transplanted into the brains of immunodeficient mice, without expression in either mouse brain cells or non-brain tissues. The mosaic-capsids AAV carrying a miR-dependent GE prevented GIC tumorigenesis in the brain and extended the survival time of tumor-bearing mice.

Conclusion

These data indicate that the mosaic-capsids AAV containing a miR-dependent GE represents a novel therapeutic virus for GBM with fewer side effects.

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Fig. 1: Identification of miR-219a-2-3p and miR-340-5p as candidate miRs for the miR-dependent gene expression system.
Fig. 2: GE AAV encoding miRCS induces cell-cycle arrest and cell death in GICs.
Fig. 3: miR-dependent AAV-GFP selectively express GFP in GIC brain tumor cells in NOG mice.
Fig. 4: Anti-tumorigenic activity of miR-dependent GE AAV with mosaic capsids in GIC brain tumors.

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Data availability

Additional data supporting the findings of this study are available from the corresponding author upon reasonable request.

References

  1. Stupp R, Mason WP, van den Bent MJ, Weller M, Fisher B, Taphoorn MJ, et al. Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N Engl J Med. 2005;352:987–96.

    Article  CAS  PubMed  Google Scholar 

  2. Singh SK, Clarke ID, Hide T, Dirks PB. Cancer stem cells in nervous system tumors. Oncogene. 2004;23:7267–73.

    Article  CAS  PubMed  Google Scholar 

  3. Kondo T. Brain cancer stem-like cells. Eur J Cancer. 2006;42:1237–42.

    Article  CAS  PubMed  Google Scholar 

  4. Vescovi AL, Galli R, Reynolds BA. Brain tumour stem cells. Nat Rev Cancer. 2006;6:425–36.

    Article  CAS  PubMed  Google Scholar 

  5. Singh SK, Clarke ID, Terasaki M, Bonn VE, Hawkins C, Squire J, et al. Identification of a cancer stem cell in human brain tumors. Cancer Res. 2003;63:5821–8.

    CAS  PubMed  Google Scholar 

  6. Hide T, Takezaki T, Nakatani Y, Nakamura H, Kuratsu J, Kondo T. Sox11 prevents tumorigenesis of glioma-initiating cells by inducing neuronal differentiation. Cancer Res. 2009;69:7953–9.

    Article  CAS  PubMed  Google Scholar 

  7. Hide T, Takezaki T, Nakatani Y, Nakamura H, Kuratsu J, Kondo T. Combination of a ptgs2 inhibitor and an epidermal growth factor receptor-signaling inhibitor prevents tumorigenesis of oligodendrocyte lineage-derived glioma-initiating cells. Stem Cells. 2011;29:590–9.

    Article  CAS  PubMed  Google Scholar 

  8. Kaneko S, Nakatani Y, Takezaki T, Hide T, Yamashita D, Ohtsu N, et al. Ceacam1L modulates STAT3 signaling to control the proliferation of glioblastoma-initiating cells. Cancer Res. 2015;75:4224–34.

    Article  CAS  PubMed  Google Scholar 

  9. Yamashita D, Kondo T, Ohue S, Takahashi H, Ishikawa M, Matoba R, et al. miR340 suppresses the stem-like cell function of glioma-initiating cells by targeting tissue plasminogen activator. Cancer Res. 2015;75:1123–33.

    Article  CAS  PubMed  Google Scholar 

  10. Ohtsu N, Nakatani Y, Yamashita D, Ohue S, Ohnishi T, Kondo T. Eva1 maintains the stem-like character of glioblastoma-initiating cells by activating the noncanonical NF-κB signaling pathway. Cancer Res. 2016;76:171–81.

    Article  CAS  PubMed  Google Scholar 

  11. Tárnok A, Ulrich H, Bocsi J. Phenotypes of stem cells from diverse origin. Cytom A. 2010;77:6–10.

    Article  Google Scholar 

  12. Dankner M, Gray-Owen SD, Huang YH, Blumberg RS, Beauchemin N. CEACAM1 as a multi-purpose target for cancer immunotherapy. Oncoimmunology. 2017;6:e1328336.

    PubMed  PubMed Central  Google Scholar 

  13. Echizenya S, Ishii Y, Kitazawa S, Tanaka T, Matsuda S, Watanabe E, et al. Discovery of a new pyrimidine synthesis inhibitor eradicating glioblastoma-initiating cells. Neuro Oncol. 2020;22:229–39.

    CAS  PubMed  Google Scholar 

  14. Breedveld FC, Dayer JM. Leflunomide: Mode of action in the treatment of rheumatoid arthritis. Ann Rheum Dis. 2000;59:841–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Brown BD, Venneri MA, Zingale A, Sergi L, Naldini L. Endogenous microRNA regulation suppresses transgene expression in hematopoietic lineages and enables stable gene transfer. Nat Med. 2006;12:585–91.

    Article  CAS  PubMed  Google Scholar 

  16. Sayeg MK, Weinberg BH, Cha SS, Goodloe M, Wong WW, Han X. Rationally designed microRNA-based genetic classifiers target specific neurons in the brain. ACS Synth Biol. 2015;4:788–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Todo T, Rabkin SD, Sundaresan P, Wu A, Meehan KR, Herscowitz HB, et al. Systemic antitumor immunity in experimental brain tumor therapy using a multimutated, replication-competent herpes simplex virus. Hum Gene Ther. 1999;10:2741–55.

    Article  CAS  PubMed  Google Scholar 

  18. Farshbaf M, Mojarad-Jabali S, Hemmati S, Hemmati S, Khosroushahi AY, Motasadizadeh H, et al. Enhanced BBB and BBTB penetration and improved anti-glioma behavior of bortezomib through dual-targeting nanostructured lipid carriers. J Control Release. 2022;345:371–84.

    Article  CAS  PubMed  Google Scholar 

  19. Zhu Z, Gorman MJ, McKenzie LD, Chai JN, Hubert CG, Prager BC, et al. Zika virus has oncolytic activity against glioblastoma stem cells. J Exp Med. 2017;214:2843–57.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Pupo A, Fernández A, Low SH, François A, Suárez-Amarán L, Samulski RJ. AAV vectors: The Rubik’s cube of human gene therapy. Mol Ther. 2022;30:3515–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kardani K, Sanchez Gil J, Rabkin SD. Oncolytic herpes simplex viruses for the treatment of glioma and targeting glioblastoma stem-like cells. Front Cell Infect Microbiol. 2023;13:1206111.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Brommel CM, Cooney AL, Sinn PL. Adeno-associated virus-based gene therapy for lifelong correction of genetic disease. Hum Gene Ther. 2020;31:985–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Chan KY, Jang MJ, Yoo BB, Greenbaum A, Ravi N, Wu WL, et al. Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Nat Neurosci. 2017;20:1172–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Goertsen D, Flytzanis NC, Goeden N, Chuapoco MR, Cummins A, Chen Y, et al. AAV capsid variants with brain-wide transgene expression and decreased liver targeting after intravenous delivery in mouse and marmoset. Nat Neurosci. 2022;25:106–15.

    Article  CAS  PubMed  Google Scholar 

  25. Thomas M, Klibanov AM. Enhancing polyethylenimine’s delivery of plasmid DNA into mammalian cells. Proc Natl Acad Sci USA. 2002;99:14640–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Negrini M, Wang G, Heuer A, Björklund T, Davidsson M. AAV production everywhere: A simple, fast, and reliable protocol for in-house AAV vector production based on chloroform extraction. Curr Protoc Neurosci. 2020;93:e103.

    Article  CAS  PubMed  Google Scholar 

  27. Xu J, Liao X, Wong C. Downregulations of B-cell lymphoma 2 and myeloid cell leukemia sequence 1 by microRNA 153 induce apoptosis in a glioblastoma cell line DBTRG-05MG. Int J Cancer. 2010;126:1029–35.

    Article  CAS  PubMed  Google Scholar 

  28. Rao SA, Arimappamagan A, Pandey P, Santosh V, Hegde AS, Chandramouli BA, et al. miR-219-5p inhibits receptor tyrosine kinase pathway by targeting EGFR in glioblastoma. PLoS ONE. 2013;8:e63164.

    Article  PubMed  PubMed Central  Google Scholar 

  29. Fan Y, Li Y, Zhu Y, Dai G, Wu D, Gao Z, et al. miR-301b-3p regulates breast cancer cell proliferation, migration, and invasion by targeting NR3C2. J Oncol. 2021;2021:8810517.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Yang C, Zhang S, Chang X, Huang Y, Cui D, Liu Z. MicroRNA-219a-2-3p modulates the proliferation of thyroid cancer cells via the HPSE/cyclin D1 pathway. Exp Ther Med. 2021;21:659.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Wu Z, Yang H, Colosi P. Effect of genome size on AAV vector packaging. Mol Ther. 2010;18:80–86.

    Article  CAS  PubMed  Google Scholar 

  32. Balestri F, Barsotti C, Lutzemberger L, Camici M, Ipata PL. Key role of uridine kinase and uridine phosphorylase in the homeostatic regulation of purine and pyrimidine salvage in brain. Neurochem Int. 2007;51:517–23.

    Article  CAS  PubMed  Google Scholar 

  33. Alkasalias T, Zhang J, Madapura H, Dalarun B, Reina OB, Lewensohn R, et al. Proof-of-principle studies on a strategy to enhance nucleotide imbalance specifically in cancer cells. Cell Death Discov. 2022;8:464.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. White RM, Cech J, Ratanasirintrawoot S, Lin CY, Rahl PB, Burke CJ, et al. DHODH modulates transcriptional elongation in the neural crest and melanoma. Nature. 2011;471:518–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Sykes DB, Kfoury YS, Mercier FE, Wawer MJ, Law JM, Haynes MK, et al. Inhibition of dihydroorotate dehydrogenase overcomes differentiation blockade in acute myeloid leukemia. Cell. 2016;167:171–186.e15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Brown KK, Spinelli JB, Asara JM, Toker A. Adaptive reprogramming of de novo pyrimidine synthesis is a metabolic vulnerability in triple-negative breast cancer. Cancer Discov. 2017;7:391–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Nonnenmacher M, Wang W, Child MA, Ren XQ, Huang C, Ren AZ, et al. Rapid evolution of blood-brain-barrier-penetrating AAV capsids by RNA-driven biopanning. Mol Ther Methods Clin Dev. 2020;20:366–78.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Smith LM, Nesterova A, Ryan MC, Duniho S, Jonas M, Anderson M, et al. CD133/prominin-1 is a potential therapeutic target for antibody-drug conjugates in hepatocellular and gastric cancers. Br J Cancer. 2008;99:100–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Wang Y, Chen M, Wu Z, Tong C, Dai H, Guo Y, et al. CD133-directed CAR T cells for advanced metastasis malignancies: A phase I trial. Oncoimmunology. 2018;7:e1440169.

    Article  PubMed  PubMed Central  Google Scholar 

  40. Tang L, Huang H, Tang Y, Li Q, Wang J, Li D, et al. CD44v6 chimeric antigen receptor T cell specificity towards AML with FLT3 or DNMT3A mutations. Clin Transl Med. 2022;12:e1043.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Bei Y, He J, Dong X, Wang Y, Wang S, Gou W, et al. Targeting CD44 variant 5 with an antibody-drug conjugate is an effective therapeutic strategy for intrahepatic cholangiocarcinoma. Cancer Res. 2023;83:2405–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Tibesku CO, Szuwart T, Ocken SA, Skwara A, Fuchs S. Expression of the matrix receptor CD44v5 on chondrocytes changes with osteoarthritis: An experimental investigation in the rabbit. Ann Rheum Dis. 2006;65:105–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Ma K, Xu H, Zhang J, Zhao F, Liang H, Sun H, et al. Insulin-like growth factor-1 enhances neuroprotective effects of neural stem cell exosomes after spinal cord injury via an miR-219a-2-3p/YY1 mechanism. Aging. 2019;11:12278–94.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Chen N, Peng C, Li D. Epigenetic underpinnings of inflammation: A key to unlock the tumor microenvironment in glioblastoma. Front Immunol. 2022;13:869307.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Das S, Bryan K, Buckley PG, Piskareva O, Bray IM, Foley N, et al. Modulation of neuroblastoma disease pathogenesis by an extensive network of epigenetically regulated microRNAs. Oncogene. 2013;32:2927–36.

    Article  CAS  PubMed  Google Scholar 

  46. Dirkse A, Golebiewska A, Buder T, Nazarov PV, Muller A, Poovathingal S, et al. Stem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment. Nat Commun. 2019;10:1787.

    Article  PubMed  PubMed Central  Google Scholar 

  47. Mohan A, Raj Rajan R, Mohan G, Kollenchery Puthenveettil P, Maliekal TT. Markers and reporters to reveal the hierarchy in heterogenous cancer stem cells. in heterogeneous cancer stem cells. Front Cell Dev Biol. 2021;9:668851.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Abdelfattah N, Kumar P, Wang C, Leu JS, Flynn WF, Gao R, et al. Single-cell analysis of human glioma and immune cells identifies S100A4 as an immunotherapy target. Nat Commun. 2022;13:767.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Yu K, Hu Y, Wu F, Guo Q, Qian Z, Hu W, et al. Surveying brain tumor heterogeneity by single-cell RNA-sequencing of multi-sector biopsies. Natl Sci Rev. 2020;7:1306–18.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Vermeulen L, Todaro M, de Sousa Mello F, Sprick MR, Kemper K, Perez Alea M, et al. Single-cell cloning of colon cancer stem cells reveals a multi-linega differentiation capacity. Proc Natl Acad Sci USA. 2008;105:13427–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Kondo T. Developing a novel therapeutic strategy against cancer stem cell heterogeneity and plasticity. Cancer Heterog Plast. 2024;1:0006.

    Google Scholar 

  52. Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, et al. An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis. Cell. 2023;186:4920–35.

    Article  CAS  PubMed  Google Scholar 

  53. Kawabata H, Konno A, Matsuzaki Y, Hirai H. A blood-brain barrier-penetrating AAV2 mutant created by a brain microvasculature endothelial cell-targeted AAV2 variant. Mol Ther Methods Clin Dev. 2023;29:81–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Müther N, Noske N, Ehrhardt A. Viral hybrid vectors for somatic integration - Are they the better solution? Viruses. 2009;1:1295–324.

    Article  PubMed  PubMed Central  Google Scholar 

  55. Elliott MJ, Maini RN, Feldmann M, Kalden JR, Antoni C, Smolen JS, et al. Randomised double-blind comparison of chimeric monoclonal antibody to tumour necrosis factor alpha (cA2) versus placebo in rheumatoid arthritis. Lancet. 1994;344:1105–10.

    Article  CAS  PubMed  Google Scholar 

  56. Nishimoto N, Kishimoto T. Interleukin 6: from bench to bedside. Nat Clin Pr Rheumatol. 2006;2:619–26.

    Article  CAS  Google Scholar 

  57. Werschler N, Quintard C, Nguyen S, Penninger J. Engineering next generation vascularized organoids. Atherosclerosis. 2024;398:118529.

    Article  CAS  PubMed  Google Scholar 

  58. Lavazza A. Potential ethical problems with human cerebral organoids: Consciousness and moral status of future brains in a dish. Brain Res. 2021;1750:147146.

    Article  CAS  PubMed  Google Scholar 

  59. Kataoka M, Gyngell C, Savulescu J, Sawai T. The donation of human biological material for brain organoid research: the problems of consciousness and consent. Sci Eng Ethics. 2024;30:3.

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank Dr. Feng Zhang for providing pX601-AAV-CMV NLS-SaCas9-NLS-3xHA-bGHpA;U6 BsaI-sgRNA through Addgene, and Dr. Toshio Kitamura for pMY-IRES-EGFP vector.

Funding

This work was partly supported by AMED Practical Research for Innovative Cancer Control (17ck0106236h0002), JSPS KAKENHI Grant-in-Aid for Scientific Research (20H03559), and the Joint Research Program of the Institute for Genetic Medicine Hokkaido University (all to TK).

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Contributions

TK conceived the study and designed the experiments. ZW, PZ, ZC, JH, YLS, DY and TK performed the experiments and analyzed data. ZC, JH, YLS and TK have contributed to the interpretation of the results. TK wrote the manuscript. All authors have read and approved the final version.

Corresponding author

Correspondence to Toru Kondo.

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The authors declare no competing interests.

Ethics approval and consent to participate

Five primary human glioma samples, including three GBMs, one anaplastic astrocytoma (AA), and one diffuse oligodendroglioma (DO), were collected from Ehime University Hospital. Informed consent was obtained from all patients according to the Research Ethics Committee guidelines (approval number: 1208009) and the specimens were used to prepare glioma lines, GICs (E3, E6, E16), AA, and DO. The glioma lines were used in compliance with the research guidelines of the Ehime University Graduate School of Medicine and the Institute for Genetic Medicine of Hokkaido University.

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Wang, Z., Zou, P., Chen, Z. et al. Novel strategy to target glioblastoma-initiating cells using a braintropic adeno-associated virus carrying a miR-dependent genome-editing system. Br J Cancer 132, 1100–1109 (2025). https://doi.org/10.1038/s41416-025-03007-3

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