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. 2020 May;38(5):586-599.
doi: 10.1038/s41587-020-0472-9. Epub 2020 May 11.

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

Christopher R Merritt  1 , Giang T Ong  2 , Sarah E Church  2 , Kristi Barker  2 , Patrick Danaher  2 , Gary Geiss  2 , Margaret Hoang  2 , Jaemyeong Jung  2 , Yan Liang  2 , Jill McKay-Fleisch  2 , Karen Nguyen  2 , Zach Norgaard  2 , Kristina Sorg  2 , Isaac Sprague  2 , Charles Warren  2 , Sarah Warren  2 , Philippa J Webster  2 , Zoey Zhou  2 , Daniel R Zollinger  2 , Dwayne L Dunaway  2 , Gordon B Mills  3 , Joseph M Beechem  4
Affiliations

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

Christopher R Merritt et al. Nat Biotechnol. 2020 May.

Abstract

Digital Spatial Profiling (DSP) is a method for highly multiplex spatial profiling of proteins or RNAs suitable for use on formalin-fixed, paraffin-embedded (FFPE) samples. The approach relies on (1) multiplexed readout of proteins or RNAs using oligonucleotide tags; (2) oligonucleotide tags attached to affinity reagents (antibodies or RNA probes) through a photocleavable (PC) linker; and (3) photocleaving light projected onto the tissue sample to release PC oligonucleotides in any spatial pattern across a region of interest (ROI) covering 1 to ~5,000 cells. DSP is capable of single-cell sensitivity within an ROI using the antibody readout, with RNA detection feasible down to ~600 individual mRNA transcripts. We show spatial profiling of up to 44 proteins and 96 genes (928 RNA probes) in lymphoid, colorectal tumor and autoimmune tissues by using the nCounter system and 1,412 genes (4,998 RNA probes) by using next-generation sequencing (NGS). DSP may be used to profile not only proteins and RNAs in biobanked samples but also immune markers in patient samples, with potential prognostic and predictive potential for clinical decision-making.

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References

    1. Garon, E. B. et al. Pembrolizumab for the treatment of non-small-cell lung cancer. N. Engl. J. Med. 372, 2018–2028 (2015). - DOI
    1. Yu, H. et al. PD-L1 expression by two complementary diagnostic assays and mRNA in situ hybridization in small cell lung cancer. J. Thorac. Oncol. 12, 110–120 (2017). - DOI
    1. Yu, H., Boyle, T. A., Zhou, C., Rimm, D. L. & Hirsch, F. R. PD-L1 expression in lung cancer. J. Thorac. Oncol. 11, 964–975 (2016). - DOI
    1. Ting, D. T. et al. Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 331, 593–596 (2011). - DOI
    1. Garber, K. Oncologists await historic first: a pan-tumor predictive marker, for immunotherapy. Nat. Biotechnol. 35, 297–298 (2017). - DOI

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