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

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.

A very brief history of respiratory biology

A better understanding of what life is and how living organisms function has always been of crucial importance to humans, but ‘biology’ as a scientific discipline is quite young, the term being coined around 1800. Similarly, ‘respiratory biology’ as a discrete branch of biology is much younger and even today the term is not commonly used. However, the knowledge about life and the discovery and study of respiration as parts of other disciplines accumulated as a mosaic over the centuries. Some of the most important persons and their primary achievements in the field that we now call respiratory biology are summarized in this chapter.

Respiratory Biology of Animals

The aim of this book is to shed light on one of the most fundamental processes of life in the various lineages of animals: respiration. It provides a certain background on the physiological side of respiration, but it clearly focuses on the morphological aspects. In general, the intention of this book is to illustrate the impressive diversity of respiratory faculties (form–function complexes) rather than serving as an encyclopaedic handbook. It takes the reader on a journey through the entire realm of animals and discusses the structures involved in gas exchange, how they work, and most importantly, how all of this may be connected on an evolutionary scale. Due to the common problem, namely oxygen uptake and carbon dioxide release, and the limited number of solutions, basically surface area, barrier thickness, and physical exchange model of the respiratory organ, it is not surprising that one finds a huge number of convergences. These include, for instance, the repeated origin of tubular tracheae among several lineages of arthropods, similar lung structures in snails and amphibians, and counter-current exchange gills in bivalves and fish. However, there are certain phylogenetic constraints evident and the respiratory faculty appears as a yet to be adequately exploited source of information for systematic considerations. The ultimate goal of this book is to stimulate further research in respiratory biology, because a huge number of questions remain to be tackled on all levels, ranging from molecular through functional to especially the evolutionary aspects.