SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution

PLoS Biol. 2020 Nov 20;18(11):e3000675. doi: 10.1371/journal.pbio.3000675. eCollection 2020 Nov.

Abstract

Changes in cell identities and positions underlie tissue development and disease progression. Although single-cell mRNA sequencing (scRNA-Seq) methods rapidly generate extensive lists of cell states, spatially resolved single-cell mapping presents a challenging task. We developed SCRINSHOT (Single-Cell Resolution IN Situ Hybridization On Tissues), a sensitive, multiplex RNA mapping approach. Direct hybridization of padlock probes on mRNA is followed by circularization with SplintR ligase and rolling circle amplification (RCA) of the hybridized padlock probes. Sequential detection of RCA-products using fluorophore-labeled oligonucleotides profiles thousands of cells in tissue sections. We evaluated SCRINSHOT specificity and sensitivity on murine and human organs. SCRINSHOT quantification of marker gene expression shows high correlation with published scRNA-Seq data over a broad range of gene expression levels. We demonstrate the utility of SCRINSHOT by mapping the locations of abundant and rare cell types along the murine airways. The amenability, multiplexity, and quantitative qualities of SCRINSHOT facilitate single-cell mRNA profiling of cell-state alterations in tissues under a variety of native and experimental conditions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Fluorescent Dyes
  • Humans
  • In Situ Hybridization / methods*
  • Mice
  • Nucleic Acid Amplification Techniques / methods*
  • Nucleic Acid Hybridization / methods
  • Oligonucleotides
  • RNA / chemistry
  • RNA, Messenger / metabolism
  • Single-Cell Analysis / methods*

Substances

  • Fluorescent Dyes
  • Oligonucleotides
  • RNA, Messenger
  • RNA

Grants and funding

The study was founded by the Swedish Research Council (Vetenskapsrådet, 2016-05059) and the Swedish Cancer Society (Cancerfonden, 160499) to CS. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the grant agreement No. 874656. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.