Breathing fresh air into respiratory research with single-cell rna sequencing

Michael J. Alexander, G. R. Scott Budinger, Paul A. Reyfman*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

10 Scopus citations


The complex cellular heterogeneity of the lung poses a unique challenge to researchers in the field. While the use of bulk RNA sequencing has become a ubiquitous technology in systems biology, the technique necessarily averages out individual contributions to the overall transcriptional landscape of a tissue. Single-cell RNA sequencing (scRNA-seq) provides a robust, unbiased survey of the transcriptome comparable to bulk RNA sequencing while preserving information on cellular heterogeneity. In just a few years since this technology was developed, scRNA-seq has already been adopted widely in respiratory research and has contributed to impressive advancements such as the discoveries of the pulmonary ionocyte and of a profibrotic macrophage population in pulmonary fibrosis. In this review, we discuss general technical considerations when considering the use of scRNA-seq and examine how leading investigators have applied the technology to gain novel insights into respiratory biology, from development to disease. In addition, we discuss the evolution of single-cell technologies with a focus on spatial and multi-omics approaches that promise to drive continued innovation in respiratory research.

Original languageEnglish (US)
Article number200060
Pages (from-to)1-14
Number of pages14
JournalEuropean Respiratory Review
Issue number156
StatePublished - Jun 2020

ASJC Scopus subject areas

  • Pulmonary and Respiratory Medicine


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