Multiplex digital spatial profiling of proteins and RNA in fixed tissue.

IF: 68.164

Cited by: 374

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.

Keywords

RNAscope

MALDI

MICSSS

CODEX

Gene Expression

Ultivue

Omics

Slide-seq

Spatial Transcriptomics

FISSEQ

MIBI

GeoMx DSP

IMC

MeSH terms

Computational Biology

Gene Expression Profiling

High-Throughput Nucleotide Sequencing

Humans

Proteomics

Sequence Analysis, RNA

Software

Spatial Analysis

Tissue Fixation

Authors

Merritt, Christopher R

Ong, Giang T

Church, Sarah E

Barker, Kristi

Danaher, Patrick

Geiss, Gary

Hoang, Margaret

Jung, Jaemyeong

Liang, Yan

McKay-Fleisch, Jill

Nguyen, Karen

Norgaard, Zach

Sorg, Kristina

Sprague, Isaac

Warren, Charles

Warren, Sarah

Webster, Philippa J

Zhou, Zoey

Zollinger, Daniel R

Dunaway, Dwayne L

Mills, Gordon B

Beechem, Joseph M

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