Transcriptomics and single‐cell RNA‐sequencing

Abstract

The past four decades have yielded advances in molecular biology allowing detailed characterization of the cellular genome and the transcriptome: the complete set of RNA species transcribed by a cell or tissue. Through transcriptomics and next‐generation sequencing, we can now attain an unprecedented level of detail in understanding cellular phenotypes through examining the genes expressed in specific physiological and pathological states. In this review, we provide an overview of transcriptomics and RNA‐sequencing in the analysis of whole tissue and single cells. We describe the techniques and pitfalls involved in the isolation and sequencing of single cells, and what additional benefits this application can provide. Finally, we look to how these technologies are being applied in pulmonary research, and how they may translate in the near future into clinical practice.

Silica‐related diseases in the modern world

“…AMs have been difficult to study due to intense autofluorescence and nonspecific surface markers, hampering attempts to define phenotypes through surface labelling and conventional flow cytometry. Recent technological developments that now allow description of the entire transcriptome in single cells (single‐cell RNA sequencing, scRNAseq) have overcome these obstacles, so that unprecedented description of cellular taxonomy even in complex tissues and disease states is now possible 34. This technique has unveiled the presence of an aberrant profibrotic AM, which appears central to the pathogenesis of pulmonary fibrosis, and which is characterized by overexpression of secreted phosphoprotein 1, which encodes osteopontin 35.…”

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“…Transcriptomics describes the set of mRNA molecules in one cell, tissue or organism and provide a snapshot of gene expression (which genes have been up and downregulated) [74]. Circulating blood cells may carry informative changes in their RNA expression profile which would be characteristic for internal infection or appendix inflammation [17].…”

‘Omics’: The new language in medicine that we all must learn

“…In determining the role of genomics and transcriptomics in respiratory disease, Chambers et al . provided a unique insight into single‐cell RNA analysis . The review examines how unique populations of cells expressing the same transcriptomics are clustered and could identify novel cell subsets in disease pathogenesis.…”