Name: single-cell gene expression using multiplex rt-qpcr to characterize heterogeneity of rare lymphoid populations
Uploaded: 2017-01-19T13:00:00
Description: Watch this Scientific Journal Video about Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations at JoVE.com

This work was supported by the Institut Pasteur, INSERM, Universit&#233; Paris Diderot and by the Minist&#232;re de la Recherche (to S.C.); the Association pour la Recherche sur le Cancer (to S.C. and R.G.); the REVIVE Future Investment Program and the Agence Nationale de Recherche (ANR; grant ''Twothyme'' to A.C.); ANR grant ''Myeloten'' (to R.G.); and the Institut National du Cancer (Role of the immune microenvironment during liver carcinogenesis, to R.G.). We acknowledge the Center for Human Immunology and Cytometry platform at Institut Pasteur for their support.

All animal experiments were approved of by the Pasteur Institute Safety Committee in accordance with the French Agriculture Ministry and the EU guidelines.
1. Prepare a 96-well Single-cell Sorting Plate
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	<li>Prepare pre-amplification mix in a 1.5 ml tube by adding 5.0 &#181;l of specific retro-transcription buffer, 1.3 &#181;l of low ethylenediaminetetraacetic acid (EDTA) TE buffer (10 mM TE solution, pH 8, and 0.1 mM EDTA solution; 0.2 &#181;M filtered), and 0.2 &#181;l of Taq DNA polymerase per well (<str...

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This protocol describes how to obtain exhaustive gene expression information at the clonal level. Here, we investigated liver ILC compartment heterogeneity. After single-cell sorting of different ILC populations (based on widely expressed ILC surface markers), samples were pre-amplified for specific pre-selected genes. Then, the obtained cDNA and primers were loaded onto a multiplex RT-qPCR microfluidic chip. Finally, we obtained the expression of 48 different genes from 48 single cells. Gene expression results were anal...

Over the past few years, innate lymphoid cells (ILCs) have been increasingly investigated. Despite their lack of antigen-specific receptors, they belong to the lymphoid lineage and represent important sentinels for tissue homeostasis and inflammation. ILCs are currently divided into three groups based on their expression of specific transcription factor combinations and on their ability to produce cytokines6,7.
ILCs contribute to numerous homeostatic and pathophysiological situations in diverse organs via specific cytokine production8,9. To be able to understand the role of these cells, it is important to determine the various ILC subpopulations per organ and to identify their developmental relationships. In addition, phenomena of plasticity between the different subsets have been related. By studying the heterogeneity of the cells present in one organ, it is possible to delimit their stage of maturation and to distinguish their specific functions.
To illustrate the technique of single-cell multiplex RT-qPCR, hepatic ILCs were chosen, with a particular emphasis on their heterogeneity within the same ILC group (type 1 ILC)10. First, through the use of flow cytometry, three distinct ILC populations were characterized in the liver. Group 1 ILC represents around 80% of the innate effectors, while the two other populations are rare hepatic ILC populations (less than 5% of the innate effectors). Those populations were sorted using widely expressed cell-surface markers of ILC populations. As a result, sorted ILC populations in the liver look broadly similar one to another.
Single-cell multiplex RT-qPCR has emerged as one of the best techniques to promptly investigate the heterogeneity of these populations11. Two main characteristics are determined by taking advantage of the single-cell multiplex RT-qPCR technique. First, by looking at the clonal level, it is possible to recover cell-specific gene expression for comparison between cells that apparently display similar developmental stages. Then, by looking at a pre-selected combination of gene expression, we will determine new gene signatures based on simultaneous gene expression patterns at one time point. These aspects permit the collection of a wide variety of expression data for a large number of cells, even on rare populations, since the technique is performed at the clonal level. Thereby, ILC heterogeneity in the liver can be adequately assessed.
Next, by sorting all cells with a global ILC phenotype, a wide overview of the multiple-gene expression of the liver ILC populations is obtained, even though they represent extremely rare populations. A microfluidic-based chip allows experimentation with even a small amount of cell material. As a consequence, the gene expression profiles of rare cell populations can be obtained. Using online gene signature analysis software, cell population clusters and potential cell relationships can be investigated. Consequently, functional tests can be performed to validate the clustering data at the in vivo level.
Tens of gene expressions could be assessed concomitantly on hundreds or more single cells on the same chip3,11,12. Design of the assay is the longest and most important part of the experiment. The determination of the genes relevant to the hypothesis to be tested is paramount to obtain relevant results. Secondly, internal control (such as known surface markers used for sorting) and specific controls are needed. This is crucial to test the primer amplification specificity, the efficiency of the amplification, and the absence of primer competition. Therefore, working with single-cell multiplex RT-qPCR is a timesaving technique, as multiple-gene expression of a cell is assessed at the same time.
Using the same chip and mix of reagents for all cells limits the possible errors of manipulation and allows for reproducibility between samples. Altogether, the different aspects of single-cell multiplex RT-qPCR allows for the production of highly reliable results at the clonal level, with a great level of sensitivity for a wide variety of samples and genes. The obtained results offer powerful and robust data for biostatistical tests.
This can be achieved due to the microfluidic aspect of the method, which allows for work on very small amounts of material and leads to exhaustive results. Finally, using online software, it is possible to compare the desired populations.

single-cell gene expression using multiplex rt-qpcr to characterize heterogeneity of rare lymphoid populations

Gene expression heterogeneity is an interesting feature to investigate in lymphoid populations. Gene expression in these cells varies during cell activation, stress, or stimulation. Single-cell multiplex gene expression enables the simultaneous assessment of tens of genes1,2,3. At the single-cell level, multiplex gene expression determines population heterogeneity4,5. It allows for the distinction of population heterogeneity by determining both the probable mix of diverse precursor stages among mature cells and also the diversity of cell responses to stimuli.
Innate lymphoid cells (ILC) have been recently described as a population of innate effectors of the immune response6,7. In this protocol, cell heterogeneity of the ILC hepatic compartment is investigated during homeostasis.
Currently, the most widely used technique to assess gene expression is RT-qPCR. This method measures gene expression only one gene at a time. Additionally, this method cannot estimate heterogeneity of gene expression, since multiple cells are needed for one test. This leads to the measurement of the average gene expression of the population. When assessing large numbers of genes, RT-qPCR becomes a time-, reagent-, and sample-consuming method. Hence, the trade-offs limit the number of genes or cell populations that can be evaluated, increasing the risk of missing the global picture.
This manuscript describes how single-cell multiplex RT-qPCR can be used to overcome these limitations. This technique has benefited from recent microfluidics technological advances1,2. Reactions occurring in multiplex RT-qPCR chips do not exceed the nanoliter-level. Hence, single-cell gene expression, as well as simultaneous multiple gene expression, can be performed in a reagent-, sample-, and cost-effective manner. It is possible to test cell gene signature heterogeneity at the clonal level between cell subsets within a population at different developmental stages or under different conditions4,5. Working on rare populations with large numbers of conditions at the single-cell level is no longer a restriction.

Lymphoid populations display great diversity in gene expression. In this protocol, liver ILC compartment heterogeneity was investigated using single-cell multiplex RT-qPCR gene expression. Unlike other gene expression techniques, single-cell multiplex RT-qPCR gene expression allows work on several populations, even the rarest, at the same time. This specificity, coupled with a high sensitivity at the clonal level, allows for the investigation of differences in gene signatures within a pop...

Watch this Scientific Journal Video about Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations at JoVE.com

Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations

This protocol describes how to assess the expression of a large array of genes at the clonal level. Single-cell RT-qPCR produces highly reliable results with a strong sensitivity for hundreds of samples and genes.

Gene expression heterogeneity is an interesting feature to investigate in lymphoid populations. Gene expression in these cells varies during cell ...

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