Multiplex digital spatial profiling of proteins and RNA in fixed tissue
| Autor: | Zoey Zhou, Kristi Barker, Margaret L. Hoang, Isaac Sprague, Chris Merritt, Sarah Warren, Patrick Danaher, Yan Liang, Giang T. Ong, Karen Nguyen, Daniel R. Zollinger, Joseph M. Beechem, Dwayne Dunaway, Kristina Sorg, Gary K. Geiss, Gordon B. Mills, Sarah E. Church, Charles Warren, Philippa J. Webster, Jaemyeong Jung, Zach Norgaard, Jill McKay-Fleisch |
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| Rok vydání: | 2019 |
| Předmět: |
Proteomics
Tissue Fixation Sequence analysis High-throughput screening Biomedical Engineering Bioengineering Computational biology Applied Microbiology and Biotechnology 03 medical and health sciences 0302 clinical medicine Humans Multiplex Gene 030304 developmental biology 0303 health sciences Messenger RNA Spatial Analysis Oligonucleotide Chemistry Sequence Analysis RNA Gene Expression Profiling RNA Computational Biology High-Throughput Nucleotide Sequencing Molecular Medicine Linker 030217 neurology & neurosurgery Software Biotechnology |
| Zdroj: | Nature biotechnology. 38(5) |
| ISSN: | 1546-1696 |
| Popis: | 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. A turnkey system allows for spatial profiling of proteins and RNA in fixed tissues, providing a window on cellular heterogeneity. |
| Databáze: | OpenAIRE |
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