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Single-cell mRNA cytometry via sequence-specific nanoparticle clustering and trapping


Cell-to-cell variation in gene expression creates a need for techniques that can characterize expression at the level of individual cells. This is particularly true for rare circulating tumour cells, in which subtyping and drug resistance are of intense interest. Here we describe a method for cell analysis—single-cell mRNA cytometry—that enables the isolation of rare cells from whole blood as a function of target mRNA sequences. This approach uses two classes of magnetic particles that are labelled to selectively hybridize with different regions of the target mRNA. Hybridization leads to the formation of large magnetic clusters that remain localized within the cells of interest, thereby enabling the cells to be magnetically separated. Targeting specific intracellular mRNAs enablescirculating tumour cells to be distinguished from normal haematopoietic cells. No polymerase chain reaction amplification is required to determine RNA expression levels and genotype at the single-cell level, and minimal cell manipulation is required. To demonstrate this approach we use single-cell mRNA cytometry to detect clinically important sequences in prostate cancer specimens.

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Fig. 1: Cellular mRNA analysis approach.
Fig. 2: Cell capture and profiling mediated by mRNA-directed magnetic nanoparticles.
Fig. 3: Analysis of clinically relevant mRNAs.
Fig. 4: Analysis of clinical samples.


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Research reported in this publication was supported by the Canadian Institutes of Health Research (grant no. FDN-148415), the Natural Sciences and Engineering Research Council of Canada (grant no. 2016-06090), the Province of Ontario through the Ministry of Research, Innovation and Science (grant no. RE05-009), and the National Cancer Institute of the National Institutes of Health (grant no. 1R33CA204574). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the other funding agencies. We also thank A. Joshua at the Princess Margaret Hospital for supplying clinical specimens.

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M.L., S.O.K. and E.H.S. conceived and designed the experiments; M.L., R.M.M., M.P., S.U.A., I.I., C.-L.H. and M.M. performed the experiments and analysed the data. All authors discussed the results and contributed to the preparation and editing of the manuscript.

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Correspondence to Shana O. Kelley.

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The authors declare no competing interests.

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Labib, M., Mohamadi, R.M., Poudineh, M. et al. Single-cell mRNA cytometry via sequence-specific nanoparticle clustering and trapping. Nature Chem 10, 489–495 (2018).

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