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Fine tuning of CpG spatial distribution with DNA origami for improved cancer vaccination

Nature Nanotechnology (2024)Cite this article

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Abstract

Multivalent presentation of ligands often enhances receptor activation and downstream signalling. DNA origami offers a precise nanoscale spacing of ligands, a potentially useful feature for therapeutic nanoparticles. Here we use a square-block DNA origami platform to explore the importance of the spacing of CpG oligonucleotides. CpG engages Toll-like receptors and therefore acts to activate dendritic cells. Through in vitro cell culture studies and in vivo tumour treatment models, we demonstrate that square blocks induce Th1 immune polarization when CpG is spaced at 3.5 nm. We observe that this DNA origami vaccine enhances DC activation, antigen cross-presentation, CD8 T-cell activation, Th1-polarized CD4 activation and natural-killer-cell activation. The vaccine also effectively synergizes with anti-PD-L1 for improved cancer immunotherapy in melanoma and lymphoma models and induces long-term T-cell memory. Our results suggest that DNA origami may serve as a platform for controlling adjuvant spacing and co-delivering antigens in vaccines.

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Fig. 1: SQB-DNA-origami-based vaccines (DoriVac) were fabricated with different spacings of CpG adjuvant.
Fig. 2: CpG, delivered at a spacing of 3.5 nm on SQB DNA origami, provides enhanced DC activation for Th1-polarized immune response.
Fig. 3: T-cell activation by DCs instructed by DoriVac bearing varying CpG spatial patterns and densities revealed distinctive anti-tumoural effects.
Fig. 4: DoriVac distribution, in vivo immune-cell stimulation and prophylactic vaccination effects.
Fig. 5: Immune-cell profiling revealed a Th1-polarized immune response after therapeutic DoriVac treatment in mouse melanoma models.
Fig. 6: DoriVac combined with immune checkpoint inhibitor anti-PD-L1 exhibited synergistic, durable T-cell responses.

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Data availability

Data supporting the findings of this study are available in the Article and its Supplementary Information. The RNAseq data for the stimulated BMDCs generated and analysed in this Article have been deposited in NCBI’s Gene Expression Omnibus under accession no. GSE251850. Source data are provided with this paper.

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Acknowledgements

We thank Q. Yan, Z. Zhao, T. Zhang, P. Lill, P. Prabhala, L. Chou, J. Han, D. Minev, B. Everhart, J. Deng, D. Zhang, K. Adu-Berchie, H. Dembele, A. Rajwar and K. Simpson for aiding in labour support, experimental design, exploring experiments and manuscript proofreading. We also thank M. Perez, M. Carr and E. Zigon for their assistance in lab management and facility usage. We thank M. Bastings and A. Li for exploration—before the current project initiated—of CpG-functionalized DNA origami barrels for immune stimulation. This work was funded by the Barr Award granted by the Claudia Adams Barr Program (Y.C.Z.) in the Dana-Farber Cancer Institute and by Wyss validation funding (Y.C.Z.) at the Wyss Institute for Biologically Inspired Engineering at Harvard. This study was supported by the Korean Fund for Regenerative Medicine (J.H.R.; 21A0504L1) funded by the Korean government (the Ministry of Science and ICT and the Korean Ministry of Health & Welfare) and the Intramural Research Program of KIST (J.H.R.; no. 2E30840). This project was also supported by an NIH U54 grant (W.M.S.; CA244726-01).

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Authors and Affiliations

  1. Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA

    Yang C. Zeng, Olivia J. Young, Christopher M. Wintersinger, Kathleen Mulligan, Ick Chan Kwon, Ju Hee Ryu & William M. Shih

  2. Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA

    Yang C. Zeng, Olivia J. Young, Frances M. Anastassacos, James I. MacDonald, Giorgia Isinelli, Haiqing Bai, Amanda R. Graveline, Andyna Vernet, Melinda Sanchez, Thomas C. Ferrante, David J. Mooney & William M. Shih

  3. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA

    Yang C. Zeng, Olivia J. Young, Christopher M. Wintersinger, Frances M. Anastassacos & William M. Shih

  4. Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA

    Olivia J. Young

  5. Department of Drug and Health Sciences, University of Catania, Catania, Italy

    Giorgia Isinelli

  6. Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA

    Maxence O. Dellacherie, Miguel Sobral & David J. Mooney

  7. Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea

    Youngjin Choi, Ick Chan Kwon & Ju Hee Ryu

  8. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA

    Derin B. Keskin & Catherine J. Wu

  9. Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA

    Geoffrey G. Fell & Donna Neuberg

  10. KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea

    Ick Chan Kwon

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  1. Yang C. Zeng
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Contributions

Y.C.Z. developed and planned the experiments, carried out the vaccine fabrication and validation, and wrote the manuscript. J.H.R. and W.M.S. provided the experimental and theoretical guidance and edited the manuscript. O.J.Y. assisted Y.C.Z. in performing the experiments, analysing the data and manuscript editing. C.M.W., F.M.A., J.I.M. and G.I. assisted with the DNA origami design, modelling and fabrication. H.B. performed the RNAseq analysis. M.O.D., M. Sobral, M. Sanchez, A.R.G. and A.V. helped with the animal study design, modelling and sampling. T.C.F. assisted with the confocal experiment. Y.C. assisted with the 3D modelling and manuscript editing. G.G.F. and D.N. guided the statistical analysis. C.J.W. and D.B.K. guided the experiment design and offered manuscript editing. D.J.M. and I.C.K. provided project support and manuscript editing.

Corresponding authors

Correspondence to Ju Hee Ryu or William M. Shih.

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Competing interests

W.M.S., J.H.R. and Y.C.Z. are inventors on US patent application PCT/US2020/036281 held by Dana-Farber Cancer Institute, Korea Institute of Science and Technology and Wyss Institute (filed on 5 June 2020) partially based on this work. All other authors declare no competing interests.

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Nature Nanotechnology thanks Mark Bathe, Diana Morzy and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–34, Tables 1–6, Discussion and Methods.

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Supplementary Information

Supplementary Video 1 This video demonstrates the effective uptake of DNA origami nanoparticles coated with K10-PEG5k by DCs within a time frame of 2 h and reveals the presence of DNA origami nanoparticles (pink) conjugated with OVA antigen (green) within the DCs, along with late endosomes (cyan).

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Zeng, Y.C., Young, O.J., Wintersinger, C.M. et al. Fine tuning of CpG spatial distribution with DNA origami for improved cancer vaccination. Nat. Nanotechnol. (2024). https://doi.org/10.1038/s41565-024-01615-3

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