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Optimizing CpG spatial distribution with DNA origami for Th1-polarized therapeutic vaccination

Yang C. Zeng, Olivia J. Young, Christopher M. Wintersinger, Frances M. Anastassacos, James I. MacDonald, Giorgia Isinelli, Maxence O. Dellacherie, Miguel Sobral, View ORCID ProfileHaiqing Bai, Amanda R. Graveline, Andyna Vernet, Melinda Sanchez, Kathleen Mulligan, Youngjin Choi, Thomas C. Ferrante, Derin B. Keskin, Geoffrey G. Fell, Donna Neuberg, Catherine J. Wu, David J. Mooney, Ick Chan Kwon, Ju Hee Ryu, William M. Shih
doi: https://doi.org/10.1101/2022.06.08.495340
Yang C. Zeng
1Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
4Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Olivia J. Young
1Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
4Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
7Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Christopher M. Wintersinger
1Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
4Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Frances M. Anastassacos
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
4Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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James I. MacDonald
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
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Giorgia Isinelli
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
8Department of Drug and Health Sciences, University of Catania, Catania, Italy
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Maxence O. Dellacherie
5Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
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Miguel Sobral
5Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
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Haiqing Bai
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
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  • ORCID record for Haiqing Bai
Amanda R. Graveline
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
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Andyna Vernet
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
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Melinda Sanchez
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
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Kathleen Mulligan
1Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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Youngjin Choi
2Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
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Thomas C. Ferrante
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
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Derin B. Keskin
6Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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Geoffrey G. Fell
9Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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Donna Neuberg
9Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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Catherine J. Wu
6Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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David J. Mooney
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
5Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
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Ick Chan Kwon
1Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
2Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
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Ju Hee Ryu
1Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
2Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
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  • For correspondence: william.shih@wyss.harvard.edu jhryu@kist.re.kr
William M. Shih
1Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
3Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
4Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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  • For correspondence: william.shih@wyss.harvard.edu jhryu@kist.re.kr
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Abstract

Multivalent presentation of ligands often enhances receptor activation and downstream signaling. DNA origami offers precise nanoscale spacing of ligands, a potentially useful feature for therapeutic nanoparticles. Here we introduce a “square block” DNA origami platform to explore the importance of spacing of CpG oligonucleotides, which engage Toll-like receptors and thereby act as danger signals for dendritic cells. Through in vitro cell-culture studies and in vivo tumor-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 NK cell activation. The vaccine also synergizes effectively 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 an advanced vaccine platform for controlling adjuvant spacing and co-delivering antigens.

One Sentence Summary This study developed a DNA origami-based cancer vaccine (DoriVac) that co-delivers antigen and CpG immune adjuvant with an optimal spacing for Th1 immune polarization.

Competing Interest Statement

W.M.S, J.H.R. and Y.C.Z. are inventors on U.S. patent application PCT/US2020/036281 held by Dana-Farber Cancer Institute, Korea Institute of Science & Technology, and Wyss Institute (filed on 6/5/2020) partially based on this work. All other authors declare that they have no competing interests.

Footnotes

  • In this revised manuscript, we have performed the following experiments over the last year, specifically: 1.We have included confocal images colocalizing the DNA origami vaccine and endosomes 2.We have validated the spacing effects on human pDCs, human moDCs and mouse RAW264.7 cells. 3.We have compared DoriVac with liposomes carrying the same amount of antigen and adjuvant. DoriVac showed 12 times more SIINFEKL MHC I expression on the RAW264.7 cells. 4.We have investigated more signaling pathways and identified that TLR13 might also become involved in DC activation in mouse BMDCs. 5.We have evaluated the vaccine distribution to the draining LN and clearance by liver and kidney. 6.We have investigated neoantigen conjugated vaccine in B16F10 mouse model and identified that NK cells were also highly activated in DoriVac applied groups. 7.We have profiled cytokines in the blood after three doses of vaccination and observed significant increases of type 1 cytokines. 8.We also have tested the vaccine efficacy in a lymphoma model and validated the durable CD8 and CD4 T cell responses.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 27, 2022.
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Optimizing CpG spatial distribution with DNA origami for Th1-polarized therapeutic vaccination
Yang C. Zeng, Olivia J. Young, Christopher M. Wintersinger, Frances M. Anastassacos, James I. MacDonald, Giorgia Isinelli, Maxence O. Dellacherie, Miguel Sobral, Haiqing Bai, Amanda R. Graveline, Andyna Vernet, Melinda Sanchez, Kathleen Mulligan, Youngjin Choi, Thomas C. Ferrante, Derin B. Keskin, Geoffrey G. Fell, Donna Neuberg, Catherine J. Wu, David J. Mooney, Ick Chan Kwon, Ju Hee Ryu, William M. Shih
bioRxiv 2022.06.08.495340; doi: https://doi.org/10.1101/2022.06.08.495340
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Optimizing CpG spatial distribution with DNA origami for Th1-polarized therapeutic vaccination
Yang C. Zeng, Olivia J. Young, Christopher M. Wintersinger, Frances M. Anastassacos, James I. MacDonald, Giorgia Isinelli, Maxence O. Dellacherie, Miguel Sobral, Haiqing Bai, Amanda R. Graveline, Andyna Vernet, Melinda Sanchez, Kathleen Mulligan, Youngjin Choi, Thomas C. Ferrante, Derin B. Keskin, Geoffrey G. Fell, Donna Neuberg, Catherine J. Wu, David J. Mooney, Ick Chan Kwon, Ju Hee Ryu, William M. Shih
bioRxiv 2022.06.08.495340; doi: https://doi.org/10.1101/2022.06.08.495340

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