Limits...
Genetics and immunity in the era of single-cell genomics

View Article: PubMed Central - PubMed

ABSTRACT

Recent developments in the field of single-cell genomics (SCG) are changing our understanding of how functional phenotypes of cell populations emerge from the behaviour of individual cells. Some of the applications of SCG include the discovery of new gene networks and novel cell subpopulations, fine mapping of transcription kinetics, and the relationships between cell clonality and their functional phenotypes. Immunology is one of the fields that is benefiting the most from such advancements, providing us with completely new insights into mammalian immunity. In this review, we start by covering new immunological insights originating from the use of single-cell genomic tools, specifically single-cell RNA-sequencing. Furthermore, we discuss how new genetic study designs are starting to explain inter-individual variation in the immune response. We conclude with a perspective on new multi-omics technologies capable of integrating several readouts from the same single cell and how such techniques might push our biological understanding of mammalian immunity to a new level.

No MeSH data available.


Related in: MedlinePlus

The current workflow of single-cell genomic methods in genetics, epigenetics and transcriptomics, and emerging combined multi-omic technologies from the same single cell. A typical workflow starts with single cell capture through either traditional FACS, microfluidics capture or microdroplets. Then DNA or RNA is prepared for sequencing by different protocols based on the aims of the study and the area of interest (genetics, epigenetics or transcriptomics). Computational analyses are used later on to extract interesting biological information. Recent emerging technologies allow combined genetics-transcriptomics and epigenetics-transcriptomics investigation from the same cell.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5036872&req=5

ddw192-F2: The current workflow of single-cell genomic methods in genetics, epigenetics and transcriptomics, and emerging combined multi-omic technologies from the same single cell. A typical workflow starts with single cell capture through either traditional FACS, microfluidics capture or microdroplets. Then DNA or RNA is prepared for sequencing by different protocols based on the aims of the study and the area of interest (genetics, epigenetics or transcriptomics). Computational analyses are used later on to extract interesting biological information. Recent emerging technologies allow combined genetics-transcriptomics and epigenetics-transcriptomics investigation from the same cell.

Mentions: At the moment, the development of new methods is a very active area of research in the field of SCG (1,2,72). Many traditional genome-wide assays are now possible at the single-cell level (73–81) (Fig. 2), and combined omic methods from the same cell are now becoming available. Dey et al developed a combined genomic DNA and mRNA sequencing (DR-Seq) method (82), and Macaulay et al developed a ‘genome and transcriptome’ sequencing (G&T-seq) method (83). Both methods combine whole genome amplification and whole transcriptome amplification to investigate genomic DNA and mRNA from the same cell, which makes the integration of genetic and transcriptional data at the single-cell level feasible. In a more recent study, Angermueller et al developed the scM&T-seq method (84), which was based on G&T-seq where a bisulphite convention was performed after the physical separation of genomic DNA from mRNA. This enables the investigation of DNA methylation and gene expression from the same cell.Figure 2.


Genetics and immunity in the era of single-cell genomics
The current workflow of single-cell genomic methods in genetics, epigenetics and transcriptomics, and emerging combined multi-omic technologies from the same single cell. A typical workflow starts with single cell capture through either traditional FACS, microfluidics capture or microdroplets. Then DNA or RNA is prepared for sequencing by different protocols based on the aims of the study and the area of interest (genetics, epigenetics or transcriptomics). Computational analyses are used later on to extract interesting biological information. Recent emerging technologies allow combined genetics-transcriptomics and epigenetics-transcriptomics investigation from the same cell.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036872&req=5

ddw192-F2: The current workflow of single-cell genomic methods in genetics, epigenetics and transcriptomics, and emerging combined multi-omic technologies from the same single cell. A typical workflow starts with single cell capture through either traditional FACS, microfluidics capture or microdroplets. Then DNA or RNA is prepared for sequencing by different protocols based on the aims of the study and the area of interest (genetics, epigenetics or transcriptomics). Computational analyses are used later on to extract interesting biological information. Recent emerging technologies allow combined genetics-transcriptomics and epigenetics-transcriptomics investigation from the same cell.
Mentions: At the moment, the development of new methods is a very active area of research in the field of SCG (1,2,72). Many traditional genome-wide assays are now possible at the single-cell level (73–81) (Fig. 2), and combined omic methods from the same cell are now becoming available. Dey et al developed a combined genomic DNA and mRNA sequencing (DR-Seq) method (82), and Macaulay et al developed a ‘genome and transcriptome’ sequencing (G&T-seq) method (83). Both methods combine whole genome amplification and whole transcriptome amplification to investigate genomic DNA and mRNA from the same cell, which makes the integration of genetic and transcriptional data at the single-cell level feasible. In a more recent study, Angermueller et al developed the scM&T-seq method (84), which was based on G&T-seq where a bisulphite convention was performed after the physical separation of genomic DNA from mRNA. This enables the investigation of DNA methylation and gene expression from the same cell.Figure 2.

View Article: PubMed Central - PubMed

ABSTRACT

Recent developments in the field of single-cell genomics (SCG) are changing our understanding of how functional phenotypes of cell populations emerge from the behaviour of individual cells. Some of the applications of SCG include the discovery of new gene networks and novel cell subpopulations, fine mapping of transcription kinetics, and the relationships between cell clonality and their functional phenotypes. Immunology is one of the fields that is benefiting the most from such advancements, providing us with completely new insights into mammalian immunity. In this review, we start by covering new immunological insights originating from the use of single-cell genomic tools, specifically single-cell RNA-sequencing. Furthermore, we discuss how new genetic study designs are starting to explain inter-individual variation in the immune response. We conclude with a perspective on new multi-omics technologies capable of integrating several readouts from the same single cell and how such techniques might push our biological understanding of mammalian immunity to a new level.

No MeSH data available.


Related in: MedlinePlus