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A nanoparticle formula for delivering siRNA or miRNAs to tumor cells in cell culture and in vivo

Nature Protocols volume 9, pages 1900–1915 (2014)Cite this article

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Abstract

To improve RNA delivery, we present a protocol to produce an RNA carrier based on a Zn(II)-dipicolylamine (Zn-DPA) analog, which is an artificial receptor for phosphate anion derivatives. We further functionalized this Zn-DPA analog to hyaluronic acid (HA)-based self-assembled nanoparticles (HA-NPs) with a hydrodynamic diameter of 100 nm by conjugating amine-functionalized Zn-DPA molecules onto the HA-NPs through amide formation, resulting in efficient tumor-targeted delivery of RNAs (siRNAs, miRNA or other short oligoribonucleotides) and small-molecule drugs. The functional group of Zn-DPA can be converted into other groups such as a carboxylic or thiol group, and the DPA analog can be covalently attached to a variety of existing and novel platforms or formulations for the development of multifunctional materials via standard bioconjugation techniques. Protocols for RNA formulation and delivery into tumor tissues and tumor cells are also described. Our design strategy offers a versatile and practical method for delivering both RNA and chemotherapeutics to tumor cells and expands existing nanomaterial capabilities to further the field of drug and gene delivery.

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Figure 1: Flow diagram of the general procedure.
Figure 2: Synthesis of bis-DPA.
Figure 3: Synthesis scheme of aminoethyl 5β-cholanoamide 5 (EtCA) and HA-aminoethyl 5β-cholanoamide (HA-CA) conjugate 6.
Figure 4: Synthesis scheme of bis-DPA-functionalized HA nanoparticles (HDz-NPs).
Figure 5: TLC analysis of compound 2.
Figure 6: Formulation of RNAs with CaP-HDz-NPs.
Figure 7: In vitro RNA transfection effect of CaP-HDz/RNA-NFs.
Figure 8: In vivo gene silencing effect of CaP-HDz/RNA-NFs.

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Acknowledgements

This work was supported in part by the National Basic Research Program of China (973 program nos. 2013CB733802 and 2014CB744503), the National Science Foundation of China (nos. 51273165, 81101101 and 81371596), an AXA Research Fund Postdoctoral Fellowship, the National Research Foundation of Korea (NRF) Postdoctoral Fellowship (no. 2013R1A6A3A03) and NRF grant (2009—0080734) from the Ministry of Education, Science and Technology (MEST, Korea), and the Intramural Research Program of the National Institute of Biomedical Imaging and Bioengineering (NIBIB), US National Institutes of Health (NIH).

Author information

Author notes

  1. Ki Young Choi, Oscar F Silvestre and Xinglu Huang: These authors contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), US National Institutes of Health (NIH), Bethesda, Maryland, USA

    Ki Young Choi, Oscar F Silvestre, Xinglu Huang, Naoki Hida, Gang Liu, Don N Ho, Seulki Lee & Xiaoyuan Chen

  2. Department of Chemical Engineering and the David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Ki Young Choi

  3. Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Fujian, Xiamen, China

    Gang Liu

  4. Department of Radiology, the Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Seulki Lee

  5. Department of Chemistry, Seoul National University, Seoul, Korea

    Sang Wook Lee & Jong In Hong

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Contributions

S.L. and X.C. conceived and designed the experiments; K.Y.C., G.L., X.H., O.F.S. and N.H. conducted the synthesis, prepared formulas and performed the biological experiments; S.W.L. and J.I.H. provided DPA analogs and summarized synthetic protocols; K.Y.C., D.N.H. and X.C. co-wrote the paper.

Corresponding author

Correspondence to Xiaoyuan Chen.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Chemical structure and 1H NMR spectrum of compound 5.

(300 MHz, CD3OD). δ=3.31(m, 2H), 2.82 (m, 2H), 1.05-0.95 (m, 6H), 0.73(s, 3H)

Supplementary Figure 2 Chemical structure and 1H NMR spectrum of compound 6.

(300 MHz, D2O/CD3OD). δ=6.8-8.3 ppm (methylene groups of the ring structure in bis-DPA), 2.0 ppm (the methyl group at the C2 position of N-acetyl glucosamine in HA), 0.6-1.8 ppm (methyl and methylene groups of the ring structure in CA).This figure is adapted from previously published work and reproduced with permission from ACS Publications.11

Supplementary Figure 3 In vitro characterizations of CaP-HDz/siRNA-NP formulations.

Size distributions (a) and zeta potential results (b) of HDz-NP, HDz/siRNA-NP, Ca-HDz/siRNA-NP and CaP-HDz/siRNA-NP. c, Release of siRNA from HDz/siRNA with the addition of phosphate ions. This figure is adapted from previously published work and reproduced with permission from ACS Publications.11

Supplementary Figure 4 Cellular uptake of RNA complexed CaP-HDz-NPs.

Celluar images of HCT116 cells treated with Cy3-siRNA complexed with CaP-HDz-NP or Lipofectamine 2000 (Lipo2K); CD44-blocked cells treated with CaP-HDz/siRNA or Cy3-siRNA only. Blue (DAPI, nuclei) and red (Cy3-siRNA). The cells treated with CaP-HDz/siRNA exhibited signifinantly stronger fluorescence signal than the cells incubated with Lipo2K/siRNA. After CD44 receptors on the cell surface were blocked by pre-treatment of excess HA molecules, fluorescence signals from siRNA were rarely detected, indicating cell-permeation of CaP-HDz/siRNA is highly dependant on the interaction between HA backbone of the NPs and CD44 cell surface receptors. This figure is adapted from previously published work and reproduced with permission from ACS Publications.11

Supplementary Figure 5 Cellular uptake of RNA/drug incorporated CaP-HDz-NPs.

Multi-channel confocal fluorescence images of HCT116 cells treated with Cy5.5-labeled CaP-HDz-NP complexed with Cy3-siRNA and loaded with Oregon green-conjugated paclitaxel (OG-PTX).Considerable amount of CaP-HDz-NP was internalized into the HCT116 cells along with miRNA and PTX. The three major components (PTX/siRNA/CaP-HDz) were co-localized in the cells at early time points (30 min after the treatement). Scale bar 15 um. This figure is adapted from previously published work and reproduced with permission from ACS Publications.11

Supplementary Figure 6 In vitro RNA transfection effect of CaP-HDz/RNA-NFs.

a, Suppression of fLuc gene expression of 143B-fLuc cells after treatment with siNC only, CaP-HDz-NP/siNC or Lipo2K/siNC fLuc gene expression and viability of 143B-fLuc cells after treatment with siRNA only, CaP-HDz-NP or Lipo2K complexed group at high concentrations. b, cell viability after treatment with siLuc, Lipo2K/siLuc and Cap-HDz/siLuc. c, cell viability after treatment with siNC, Lipo2K/siNC, and CaP-HDz-NP/siNC (*p < 0.005, **p < 0.05). The CaP-HDz-NP group shows less toxicity compared to that of the Lipo2K group. This figure is adapted from previously published work and reproduced with permission from ACS Publications.11

Supplementary information

Supplementary Figure 1

Chemical structure and 1H NMR spectrum of compound 5. (PDF 328 kb)

Supplementary Figure 2

Chemical structure and 1H NMR spectrum of compound 6. (PDF 283 kb)

Supplementary Figure 3

In vitro characterizations of CaP-HDz/siRNA-NP formulations. (PDF 118 kb)

Supplementary Figure 4

Cellular uptake of RNA complexed CaP-HDz-NPs. (PDF 546 kb)

Supplementary Figure 5

Cellular uptake of RNA/drug incorporated CaP-HDz-NPs. (PDF 85 kb)

Supplementary Figure 6

In vitro RNA transfection effect of CaP-HDz/RNA-NFs. (PDF 83 kb)

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Choi, K., Silvestre, O., Huang, X. et al. A nanoparticle formula for delivering siRNA or miRNAs to tumor cells in cell culture and in vivo. Nat Protoc 9, 1900–1915 (2014). https://doi.org/10.1038/nprot.2014.128

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