Impact of single‐cell RNA sequencing on understanding immune regulation

Abstract

The earliest single-cell transcription technique can only detect a handful of genes in a single cell with relatively low throughput. 1 Historically, scRNA-seq was applied when limited by the number of biological materials such as cells from early embryonic development. 2 It was not until 2009 that the single-cell transcriptome was combined with high-throughput sequencing, which allowed for improved throughput of gene detection and more detected transcripts than chips. 3 The impact of scRNA-seq has grown rapidly since 'single-cell sequencing' was selected as the method of 2013, mainly because of its high throughput of droplet or combinatorial indexing approaches and its wide use of advanced equipment, reagents and analysis tools. 4 In recent years, scRNA-seq has developed remarkably in the immune systems with the identification of transcriptionally distinct cell types unknown before, which has helped biologists obtain deeper insights into their research areas. [5][6][7][8] There are many distinct cell lineages localizing in primary and secondary lymphoid organs in immune systems. They also exist in tissues throughout the body and have dynamic abilities to migrate through the peripheral blood. 9 Recent advances in scRNA-seq and sophisticated bioinformatic methods have renewed our eyes on understanding immunology, which may help us reveal novel therapeutic targets from individual cells masked previously by bulk analysis.

Manual cell selection in single cell transcriptomics using scSELpy supports the analysis of immune cell subsets

“…Single cell RNA sequencing has revolutionized immunological research and has helped to substantially increase the resolution of immune cell phenotyping ( 14 ). However, this comes at the cost of complex in silico analyses to be performed.…”

“…Technological advances and also the introduction of novel therapeutic approaches ( 11 – 13 ) into the clinics have led to unprecedented insights into the regulation of aberrant immune responses in chronic inflammation in general and IBD in particular. In this context, the single cell RNA-sequencing (scRNA-seq) technology has become a popular and indispensable technique for interrogating the transcriptome on single cell level and for resolving the heterogeneity of various subsets of adaptive and innate immune cells involved in inflammatory networks in chronic inflammation ( 14 ). Consistently, while the first single cell being sequenced was reported in 2009 ( 15 ), more than 4000 Pubmed-indexed articles published in 2021 mention single-cell sequencing.…”

Single-Cell RNA Sequencing Reveals Alterations in Patient Immune Cells with Pulmonary Long COVID-19 Complications

“…This allows the researchers to identify different populations, including rare subsets of immune cells, and track the immune cell composition and cell type-specific gene expression changes in the presence of a disease [11,12]. Integrating scRNA-seq data with the information about the pathology and symptomatic observations of patients provides insight into the influence of the genetic profile of a population of individual cells on the activated molecular mechanisms and allows further investigation of the immune response within an acute or chronic condition [13].…”

RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

“…Major efforts using scRNA-seq have been applied to define atlases, notably for human and mouse cells 11 , 12 , with a potential for assessing cell–cell and virus-host interactions 13 , 14 facilitated by technical optimization of methodologies 8 , 15 . Other investigations have focused on specific organs, often in relation to pathologies 16 , especially cancer, immunotherapy, and cardiovascular diseases 17 – 19 . Research has focused as well on development 20 , 21 , various forms of multiomics 22 , and spatial transcriptomics 23 .…”