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. 2019 Sep;3(9):684-694.
doi: 10.1038/s41551-019-0417-0. Epub 2019 Jul 8.

Barcoded DNA nanostructures for the multiplexed profiling of subcellular protein distribution

Noah R Sundah  1   2 , Nicholas R Y Ho  2   3 , Geok Soon Lim  2   3 , Auginia Natalia  2 , Xianguang Ding  2 , Yu Liu  1   2 , Ju Ee Seet  4 , Ching Wan Chan  5   6 , Tze Ping Loh  2   7 , Huilin Shao  8   9   10   11
Affiliations

Barcoded DNA nanostructures for the multiplexed profiling of subcellular protein distribution

Noah R Sundah et al. Nat Biomed Eng. 2019 Sep.

Abstract

Massively parallel DNA sequencing is established, yet high-throughput protein profiling remains challenging. Here, we report a barcoding approach that leverages the combinatorial sequence content and the configurational programmability of DNA nanostructures for high-throughput multiplexed profiling of the subcellular expression and distribution of proteins in whole cells. The barcodes are formed by in situ hybridization of tetrahedral DNA nanostructures and short DNA sequences conjugated with protein-targeting antibodies, and by nanostructure-assisted ligation (either enzymatic or chemical) of the nanostructures and exogenous DNA sequences bound to nanoparticles of different sizes (which cause these localization sequences to differentially distribute across subcellular compartments). Compared with linear DNA barcoding, the nanostructured barcodes enhance the signal by more than 100-fold. By implementing the barcoding approach on a microfluidic device for the analysis of rare patient samples, we show that molecular subtypes of breast cancer can be accurately classified and that subcellular spatial markers of disease aggressiveness can be identified.

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References

    1. Borrebaeck, C. A. Precision diagnostics: moving towards protein biomarker signatures of clinical utility in cancer. Nat. Rev. Cancer 17, 199–204 (2017). - DOI
    1. Landegren, U., Al-Amin, R. A. & Björkesten, J. A myopic perspective on the future of protein diagnostics. New Biotechnol. 45, 14–18 (2018). - DOI
    1. Klein, A. M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187–1201 (2015). - DOI
    1. De Vlaminck, I. et al. Noninvasive monitoring of infection and rejection after lung transplantation. Proc. Natl Acad. Sci. USA 112, 13336–13341 (2015). - DOI
    1. Hughes, A. J. et al. Single-cell western blotting. Nat. Methods 11, 749–755 (2014). - DOI

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