Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling.
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IF: 9.438
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Abstract

Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene expression. Here, we describe expanding the chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probes targeting the protein-coding genes of the human and mouse transcriptomes, referred to as the human or mouse Whole Transcriptome Atlas (WTA). Human and mouse WTAs were validated in cell lines for concordance with orthogonal gene expression profiling methods in regions ranging from ∼10-500 cells. By benchmarking against bulk RNA-seq and fluorescence in situ hybridization, we show robust transcript detection down to ∼100 transcripts per region. To assess the performance of WTA across tissue and sample types, we applied WTA to biological questions in cancer, molecular pathology, and developmental biology. Spatial profiling with WTA detected expected gene expression differences between tumor and tumor microenvironment, identified disease-specific gene expression heterogeneity in histological structures of the human kidney, and comprehensively mapped transcriptional programs in anatomical substructures of nine organs in the developing mouse embryo. Digital Spatial Profiling technology with the WTA assays provides a flexible method for spatial whole transcriptome profiling applicable to diverse tissue types and biological contexts.

Keywords

Spatial Anatomic
Spatial Gene Expression

MeSH terms

Humans
Animals
Mice
In Situ Hybridization, Fluorescence
Gene Expression Profiling
Transcriptome
Tumor Microenvironment
Neoplasms

Authors

Zimmerman, Stephanie M
Fropf, Robin
Kulasekara, Bridget R
Griswold, Maddy
Appelbe, Oliver
Bahrami, Arya
Boykin, Rich
Buhr, Derek L
Fuhrman, Kit
Hoang, Margaret L
Huynh, Quoc
Isgur, Lesley
Klock, Andrew
Kutchma, Alecksandr
Lasley, Alexa E
Liang, Yan
McKay-Fleisch, Jill
Nelson, Jeffrey S
Nguyen, Karen
Piazza, Erin
Rininger, Aric
Zollinger, Daniel R
Rhodes, Michael
Beechem, Joseph M